Methods, reagents and cells for biosynthesizing compounds

ABSTRACT

This document describes biochemical pathways for producing 5-hydroxypentanoate methyl ester and pentanoic acid pentyl ester using one or more of a fatty acid O-methyltransferase, an alcohol O-acetyltransferase, and a monooxygenase, as well as recombinant hosts expressing one or more of such exogenous enzymes. 5-hydroxypentanoate methyl esters and pentanoic acid pentyl esters can be enzymatically converted to glutaric acid, 5-aminopentanoate, 5-hydroxypentanoate, cadaverine, or 1,5-pentanediol.

CROSS REFERENCE TO RELATED APPLICATIONS

This application claims the benefit of U.S. Provisional Application Ser. Nos. 62/012,659, filed Jun. 16, 2014, 62/012,666, filed Jun. 16, 2014, and 62/012,604, filed Jun. 16, 2014, the disclosures of each of which are incorporated herein by reference in their entirety.

TECHNICAL FIELD

This invention relates to methods for biosynthesizing 5-hydroxypentanoate methyl ester and pentanoic acid pentyl ester using one or more isolated enzymes such as a fatty acid O-methyltransferase, an alcohol O-acetyltransferase, and a monooxygenase, and to recombinant host cells expressing one or more such enzymes. This invention also relates to methods for enzymatically converting 5-hydroxypentanoate methyl ester and pentanoic acid pentyl ester to 5-hydroxypentanoate and 1,5-pentanediol using one or more enzymes such as an a monooxygenase, a demethylase, or an esterase, and recombinant hosts expressing one or more such enzymes. In addition, this invention relates to enzymatically converting 5-hydroxypentanoate and/or 1,5-pentanediol to glutaric acid, 5-aminopentanoic acid, cadaverine or 1,5-pentanediol (hereafter “C5 building blocks) and recombinant hosts producing such C5 building blocks.

BACKGROUND

Nylons are polyamides which are generally synthesized by the condensation polymerization of a diamine with a dicarboxylic acid. Similarly, Nylons may be produced by the condensation polymerization of lactams. A ubiquitous nylon is Nylon 6,6, which is produced by condensation polymerization of hexamethylenediamine (HMD) and adipic acid. Nylon 6 can be produced by a ring opening polymerization of caprolactam (Anton & Baird, Polyamides Fibers, Encyclopedia of Polymer Science and Technology, 2001).

Nylon 5 and Nylon 5,5 represent novel polyamides with value-added characteristics compared to Nylon 6 and Nylon 6,6. Nylon 5 is produced by polymerisation of 5-aminopentanoic acid, whereas Nylon 5,5 is produced by condensation polymerisation of glutaric acid and cadaverine. No economically viable petrochemical routes exist to producing the monomers for Nylon 5 and Nylon 5,5.

Given no economically viable petrochemical monomer feedstocks, biotechnology offers an alternative approach via biocatalysis. Biocatalysis is the use of biological catalysts, such as enzymes, to perform biochemical transformations of organic compounds.

Both bioderived feedstocks and petrochemical feedstocks are viable starting materials for the biocatalysis processes.

Accordingly, against this background, it is clear that there is a need for sustainable methods for producing one or more of glutaric acid, 5-hydroxypentanoate, 5-aminopentanoate, cadaverine and 1,5-pentanediol (hereafter “C5 building blocks”) wherein the methods are biocatalyst based.

However, no wild-type prokaryote or eukaryote naturally overproduces or excretes such C5 building blocks to the extracellular environment. Nevertheless, the metabolism of glutaric acid has been reported.

The dicarboxylic acid glutaric acid is converted efficiently as a carbon source by a number of bacteria and yeasts via β-oxidation into central metabolites. Decarboxylation of Coenzyme A (CoA) activated glutarate to crotonyl-CoA facilitates further catabolism via β-oxidation.

The optimality principle states that microorganisms regulate their biochemical networks to support maximum biomass growth. Beyond the need for expressing heterologous pathways in a host organism, directing carbon flux towards C5 building blocks that serve as carbon sources rather than as biomass growth constituents, contradicts the optimality principle. For example, transferring the 1-butanol pathway from Clostridium species into other production strains has often fallen short by an order of magnitude compared to the production performance of native producers (Shen et al., Appl. Environ. Microbiol., 2011, 77(9):2905-2915).

The efficient synthesis of the seven carbon aliphatic backbone precursor is a key consideration in synthesizing one or more C5 building blocks prior to forming terminal functional groups, such as carboxyl, amine or hydroxyl groups, on the C5 aliphatic backbone.

SUMMARY

This document is based at least in part on the discovery that it is possible to construct biochemical pathways for producing a seven carbon chain aliphatic backbone precursor in which one or two functional groups, i.e., carboxyl, amine, or hydroxyl, can be formed, leading to the synthesis of one or more of glutaric acid, 5-aminopentanoate, 5-hydroxypentanoate, cadaverine, and 1,5-pentanediol (hereafter “C5 building blocks). Glutaric acid and glutarate, 5-hydroxypentanoic acid and 5-hydroxypentanoate, and 5-aminopentanoic and 5-aminopentanoate are used interchangeably herein to refer to the relevant compound in any of its neutral or ionized forms, including any salt forms thereof. It is understood by those skilled in the art that the specific form will depend on pH.

One of skill in the art understands that compounds containing carboxylic acid groups (including, but not limited to, organic monoacids, hydroxyacids, aminoacids, and dicarboxylic acids) are formed or converted to their ionic salt form when an acidic proton present in the parent compound either is replaced by a metal ion, e.g., an alkali metal ion, an alkaline earth ion, or an aluminum ion; or coordinates with an organic base. Acceptable organic bases include, but are not limited to, ethanolamine, diethanolamine, triethanolamine, tromethamine, N-methylglucamine, and the like. Acceptable inorganic bases include, but are not limited to, aluminum hydroxide, calcium hydroxide, potassium hydroxide, sodium carbonate, sodium hydroxide, and the like. A salt of the present invention is isolated as a salt or converted to the free acid by reducing the pH to below the pKa, through addition of acid or treatment with an acidic ion exchange resin.

One of skill in the art understands that compounds containing amine groups (including, but not limited to, organic amines, aminoacids, and diamines) are formed or converted to their ionic salt form, for example, by addition of an acidic proton to the amine to form the ammonium salt, formed with inorganic acids such as hydrochloric acid, hydrobromic acid, sulfuric acid, nitric acid, phosphoric acid, and the like; or formed with organic acids including, but not limited to, acetic acid, propionic acid, hexanoic acid, cyclopentanepropionic acid, glycolic acid, pyruvic acid, lactic acid, malonic acid, succinic acid, malic acid, maleic acid, fumaric acid, tartaric acid, citric acid, benzoic acid, 3-(4-hydroxybenzoyl)benzoic acid, cinnamic acid, mandelic acid, methanesulfonic acid, ethanesulfonic acid, 1,2-ethanedisulfonic acid, 2-hydroxyethanesulfonic acid, benzenesulfonic acid, 2-naphthalenesulfonic acid, 4-methylbicyclo-[2.2.2]oct-2-ene-1-carboxylic acid, glucoheptonic acid, 4,4′-methylenebis-(3-hydroxy-2-ene-1-carboxylic acid), 3-phenylpropionic acid, trimethylacetic acid, tertiary butylacetic acid, lauryl sulfuric acid, gluconic acid, glutamic acid, hydroxynaphthoic acid, salicylic acid, stearic acid, muconic acid, and the like. Acceptable inorganic bases include, but are not limited to, aluminum hydroxide, calcium hydroxide, potassium hydroxide, sodium carbonate, sodium hydroxide, and the like. A salt of the present invention is isolated as a salt or converted to the free amine by raising the pH to above the pKb through addition of base or treatment with a basic ion exchange resin.

One of skill in the art understands that compounds containing both amine groups and carboxylic acid groups (including, but not limited to, aminoacids) are formed or converted to their ionic salt form by either 1) acid addition salts, formed with inorganic acids including, but not limited to, hydrochloric acid, hydrobromic acid, sulfuric acid, nitric acid, phosphoric acid, and the like; or formed with organic acids including, but not limited to, acetic acid, propionic acid, hexanoic acid, cyclopentanepropionic acid, glycolic acid, pyruvic acid, lactic acid, malonic acid, succinic acid, malic acid, maleic acid, fumaric acid, tartaric acid, citric acid, benzoic acid, 3-(4-hydroxybenzoyl)benzoic acid, cinnamic acid, mandelic acid, methanesulfonic acid, ethanesulfonic acid, 1,2-ethanedisulfonic acid, 2-hydroxyethanesulfonic acid, benzenesulfonic acid, 2-naphthalenesulfonic acid, 4-methylbicyclo-[2.2.2]oct-2-ene-1-carboxylic acid, glucoheptonic acid, 4,4′-methylenebis-(3-hydroxy-2-ene-1-carboxylic acid), 3-phenylpropionic acid, trimethylacetic acid, tertiary butylacetic acid, lauryl sulfuric acid, gluconic acid, glutamic acid, hydroxynaphthoic acid, salicylic acid, stearic acid, muconic acid, and the like. Acceptable inorganic bases include, but are not limited to, aluminum hydroxide, calcium hydroxide, potassium hydroxide, sodium carbonate, sodium hydroxide, and the like, or 2) when an acidic proton present in the parent compound either is replaced by a metal ion, e.g., an alkali metal ion, an alkaline earth ion, or an aluminum ion; or coordinates with an organic base. Acceptable organic bases include, but are not limited to, ethanolamine, diethanolamine, triethanolamine, tromethamine, N-methylglucamine, and the like. Acceptable inorganic bases include, but are not limited to, aluminum hydroxide, calcium hydroxide, potassium hydroxide, sodium carbonate, sodium hydroxide, and the like. A salt can of the present invention is isolated as a salt or converted to the free acid by reducing the pH to below the pKa through addition of acid or treatment with an acidic ion exchange resin.

Pathways, metabolic engineering and cultivation strategies described herein can rely on producing pentanoate methyl ester from pentanoate using, for example, a fatty acid O-methyltransferase and producing 5-hydroxypentanoate methyl ester from pentanoate methyl ester using, for example, a monooxygenase. 5-hydroxypentanoate can be produced from 5-hydroxypentanoate methyl ester using, for example, a demethylase or an esterase.

Pathways, metabolic engineering and cultivation strategies described herein also can rely on producing pentanoic acid pentyl ester using, for example, an alcohol O-acetyltransferase and producing 5-hydroxypentanoic acid pentyl ester, 5-hydroxypentanoic acid 5-hydroxypentyl ester and/or pentanoic acid 5-hydroxypentyl ester from pentanoic acid pentyl ester using, for example, a monooxygenase. 5-hydroxypentanoate can be produced from 5-hydroxypentanoic acid pentyl ester and/or 5-hydroxypentanoic acid 5-hydroxypentyl ester using, for example, an esterase. 1,5-pentanediol can be produced from pentanoic acid 5-hydroxypentyl ester and/or 5-hydroxypentanoic acid 5-hydroxypentyl ester using, for example, an esterase.

CoA-dependent elongation enzymes or homologs associated with the carbon storage pathways from polyhydroxyalkanoate accumulating bacteria are useful for producing precursor molecules. See, e.g., FIGS. 1-2.

In the face of the optimality principle, the inventors discovered surprisingly that appropriate non-natural pathways, feedstocks, host microorganisms, attenuation strategies to the host's biochemical network and cultivation strategies may be combined to efficiently produce one or more C5 building blocks.

In some embodiments, the C5 aliphatic backbone for conversion to a C5 building block can be formed from acetyl-CoA and propanoyl-CoA via two cycles of CoA-dependent carbon chain elongation using either NADH or NADPH dependent enzymes. See FIG. 1 and FIG. 2.

In some embodiments, an enzyme in the CoA-dependent carbon chain elongation pathway generating the C5 aliphatic backbone purposefully contains irreversible enzymatic steps.

In some embodiments, the terminal carboxyl groups can be enzymatically formed using a thioesterase, an aldehyde dehydrogenase, a 7-oxoheptanoate dehydrogenase, a 6-oxohexanoate dehydrogenase, a 5-oxopentanoate dehydrogenase or a monooxygenase. See FIG. 3 and FIG. 4.

In some embodiments, the terminal amine groups can be enzymatically formed using a ω-transaminase or a deacetylase. See FIG. 5 and FIG. 6.

In some embodiments, the terminal hydroxyl group can be enzymatically formed using a monooxygenase, an esterase, or an alcohol dehydrogenase. See FIG. 3, FIG. 7 and FIG. 8. A monooxygenase (e.g., in combination with an oxidoreductase and/or ferredoxin) or an alcohol dehydrogenase can enzymatically form a hydroxyl group. The monooxygenase can have at least 70% sequence identity to any one of the amino acid sequences set forth in SEQ ID NOs: 14-16 or 28-29. An esterase can have at least 70% identity to the amino acid sequence set forth in SEQ ID NO: 27.

A ω-transaminase or a deacetylase can enzymatically form an amine group. The ω-transaminase can have at least 70% sequence identity to any one of the amino acid sequences set forth in SEQ ID NOs. 8-13.

A thioesterase, an aldehyde dehydrogenase, a 7-oxoheptanoate dehydrogenase, a 5-oxopentanoate dehydrogenase, or a 6-oxohexanoate dehydrogenase can enzymatically form a terminal carboxyl group. The thioesterase can have at least 70% sequence identity to the amino acid sequence set forth in SEQ ID NO: 1, SEQ ID NO: 33, and/or SEQ ID NO: 34.

A carboxylate reductase (e.g., in combination with a phosphopantetheinyl transferase) can form a terminal aldehyde group as an intermediate in forming the product. The carboxylate reductase can have at least 70% sequence identity to any one of the amino acid sequences set forth in SEQ ID NOs: 2-7.

Any of the methods can be performed in a recombinant host by fermentation. The host can be subjected to a cultivation strategy under aerobic, anaerobic, or micro-aerobic cultivation conditions. The host can be cultured under conditions of nutrient limitation such as phosphate, oxygen or nitrogen limitation. The host can be retained using a ceramic membrane to maintain a high cell density during fermentation.

In any of the methods, the host's tolerance to high concentrations of a C5 building block can be improved through continuous cultivation in a selective environment.

The principal carbon source fed to the fermentation can derive from biological or non-biological feedstocks. In some embodiments, the biological feedstock is, includes, or derives from, monosaccharides, disaccharides, lignocellulose, hemicellulose, cellulose, lignin, levulinic acid and formic acid, triglycerides, glycerol, fatty acids, agricultural waste, condensed distillers' solubles, or municipal waste.

In some embodiments, the non-biological feedstock is or derives from natural gas, syngas, CO₂/H₂, methanol, ethanol, benzoate, non-volatile residue (NVR) or a caustic wash waste stream from cyclohexane oxidation processes, or a terephthalic acid/isophthalic acid mixture waste stream.

This document also features a recombinant host that includes at least one exogenous nucleic acid encoding a fatty acid O-methyltransferase and a monooxygenase, and produce 5-hydroxypentanoate methyl ester. Such a host further can include a demethylase or esterase and further produce 5-hydroxypentanoate. Such hosts further can include (i) a β-ketothiolase or an acetyl-CoA carboxylase and a β-ketoacyl-[acp] synthase, (ii) a 3-hydroxyacyl-CoA dehydrogenase or a 3-oxoacyl-CoA reductase, (iii) an enoyl-CoA hydratase, and (iv) a trans-2-enoyl-CoA reductase. The hosts also further can include one or more of a thioesterase, an aldehyde dehydrogenase, or a butanal dehydrogenase.

This document also features a recombinant host that includes at least one exogenous nucleic acid encoding an alcohol O-acetyltransferase and produce pentanoic acid pentyl ester. Such a host further can include a monooxygenase and an esterase and further produce 5-hydroxypentanoate and/or 1,5-pentanediol. Such hosts further can include (i) a β-ketothiolase or an acetyl-CoA carboxylase and a β-ketoacyl-[acp] synthase, (ii) a 3-hydroxyacyl-CoA dehydrogenase or a 3-oxoacyl-CoA reductase, (iii) an enoyl-CoA hydratase, and (iv) a trans-2-enoyl-CoA reductase. The hosts also further can include one or more of a thioesterase, a carboxylate reductase, an aldehyde dehydrogenase, a butanal or acetaldehyde dehydrogenase, or an alcohol dehydrogenase.

A recombinant host producing 5-hydroxypentanoate further can include one or more of a monooxygenase, an alcohol dehydrogenase, an aldehyde dehydrogenase, a 6-hydroxyhexanoate dehydrogenase, a 5-hydroxypentanoate dehydrogenase, a 4-hydroxybutyrate dehydrogenase, a 7-oxoheptanoate dehydrogenase, a 6-oxohexanoate dehydrogenase, or a 5-oxopentanoate dehydrogenase, the host further producing glutaric acid or glutarate semialdehyde.

A recombinant host producing 5-hydroxypentanoate further can include one or more of a monooxygenase, a transaminase, a 6-hydroxyhexanoate dehydrogenase, a 5-hydroxypentanoate dehydrogenase, a 4-hydroxybutyrate dehydrogenase, and an alcohol dehydrogenase, wherein the host further produces 5-aminopentanoate.

A recombinant host producing 5-hydroxypentanoate or 5-aminopentanoate further can include one or more of a carboxylate reductase, a ω-transaminase, a deacetylase, a N-acetyl transferase, or an alcohol dehydrogenase, the host further producing cadaverine.

A recombinant host producing 5-hydroxypentanoate further can include a carboxylate reductase or an alcohol dehydrogenase, wherein the host further produces 1,5-pentanediol.

The recombinant host can be a prokaryote, e.g., from the genus Escherichia such as Escherichia coli; from the genus Clostridia such as Clostridium ljungdahlii, Clostridium autoethanogenum or Clostridium kluyveri; from the genus Corynebacteria such as Corynebacterium glutamicum; from the genus Cupriavidus such as Cupriavidus necator or Cupriavidus metallidurans; from the genus Pseudomonas such as Pseudomonas fluorescens, Pseudomonas putida or Pseudomonas oleavorans; from the genus Delftia acidovorans, from the genus Bacillus such as Bacillus subtillis; from the genes Lactobacillus such as Lactobacillus delbrueckii; from the genus Lactococcus such as Lactococcus lactis or from the genus Rhodococcus such as Rhodococcus equi.

The recombinant host can be a eukaryote, e.g., a eukaryote from the genus Aspergillus such as Aspergillus niger; from the genus Saccharomyces such as Saccharomyces cerevisiae; from the genus Pichia such as Pichia pastoris; from the genus Yarrowia such as Yarrowia lipolytica, from the genus Issatchenkia such as Issathenkia orientalis, from the genus Debaryomyces such as Debaryomyces hansenii, from the genus Arxula such as Arxula adenoinivorans, or from the genus Kluyveromyces such as Kluyveromyces lactis.

In some embodiments, the host's endogenous biochemical network is attenuated or augmented to (1) ensure the intracellular availability of acetyl-CoA and propanoyl-CoA, (2) create a cofactor, i.e. NADH or NADPH, imbalance that may be balanced via the formation of a C5 building block, (3) prevent degradation of central metabolites, central precursors leading to and including C5 building blocks and (4) ensure efficient efflux from the cell.

Any of the recombinant hosts described herein further can include one or more of the following attenuated enzymes: polyhydroxyalkanoate synthase, an acetyl-CoA thioesterase, a propanoyl-CoA thioesterase, a methylcitrate synthase, an acetyl-CoA specific β-ketothiolase, a phosphotransacetylase forming acetate, an acetate kinase, a lactate dehydrogenase, a menaquinol-fumarate oxidoreductase, a 2-oxoacid decarboxylase producing isobutanol, an alcohol dehydrogenase forming ethanol, a triose phosphate isomerase, a pyruvate decarboxylase, a glucose-6-phosphate isomerase, a transhydrogenase dissipating the cofactor imbalance, a glutamate dehydrogenase specific for the co-factor for which an imbalance is created, a NADH/NADPH-utilizing glutamate dehydrogenase, a pimeloyl-CoA dehydrogenase; an acyl-CoA dehydrogenase accepting C5 building blocks and central precursors as substrates; a glutaryl-CoA dehydrogenase; or a pimeloyl-CoA synthetase.

Any of the recombinant hosts described herein further can overexpress one or more genes encoding: an acetyl-CoA synthetase, a 6-phosphogluconate dehydrogenase; a transketolase; a feedback resistant threonine deaminase; a puridine nucleotide transhydrogenase; a formate dehydrogenase; a glyceraldehyde-3P-dehydrogenase; a malic enzyme; a glucose-6-phosphate dehydrogenase; a fructose 1,6 diphosphatase; a propionyl-CoA synthetase; a L-alanine dehydrogenase; a L-glutamate dehydrogenase; a L-glutamine synthetase; a lysine transporter; a dicarboxylate transporter; and/or a multidrug transporter.

This document also features methods of producing a (C₃₋₈ hydroxyalkyl)-C(═O)OCH₃ ester, the method including enzymatically converting a C₄₋₉ carboxylic acid to a (C₃₋₈ alkyl)-C(═O)OCH₃ ester; and enzymatically converting the (C₃₋₈ alkyl)-C(═O)OCH₃ ester to (C₃₋₈ hydroxyalkyl)-C(═O)OCH₃ ester.

In some embodiments, the C₄₋₉ carboxylic acid can be enzymatically converted to the (C₃₋₉ alkyl)-C(═O)OCH₃ ester using a polypeptide having fatty acid O-methyltransferase activity. In some embodiments, the polypeptide having fatty acid O-methyltransferase activity is classified under EC 2.1.1.15. In some embodiments, the polypeptide having fatty acid O-methyltransferase activity can have at least 70% sequence identity to an amino acid sequence set forth in SEQ ID NO:23, SEQ ID NO:24, or SEQ ID NO:25.

In some embodiments, the (C₃₋₈ alkyl)-C(═O)OCH₃ ester can be enzymatically converted to the (C₃₋₈ hydroxyalkyl)-C(═O)OCH₃ ester using a polypeptide having monooxygenase activity. In some embodiments, the monooxygenase is classified under EC 1.14.14.- or EC 1.14.15.-. In some embodiments, the monooxygenase can have at least 70% sequence identity to an amino acid sequence set forth in SEQ ID NO: 14, SEQ ID NO: 15, SEQ ID NO: 16, SEQ ID NO:28 and/or SEQ ID NO:29.

In some embodiments, the C₄₋₉ carboxylic acid can be enzymatically produced from a C₄₋₉ alkanoyl-CoA. In some embodiments, a polypeptide having thioesterase activity can enzymatically produce the C₄₋₉ carboxylic acid from the C₄₋₉ alkanoyl-CoA. In some embodiments, the thioesterase can have at least 70% sequence identity to the amino acid sequence set forth in SEQ ID NO:1, SEQ ID NO: 33, and/or SEQ ID NO: 34. In some embodiments, a polypeptide having butanal dehydrogenase activity and a polypeptide having aldehyde dehydrogenase activity enzymatically produce the C₄₋₉ carboxylic acid from C₄₋₉ alkanoyl-CoA.

This document also features methods of producing one or more hydroxy-substituted (C₄₋₉ alkyl)-OC(═O)—(C₃₋₈ alkyl) esters. The method includes enzymatically converting a C₄₋₉ alkanoyl-CoA to a (C₄₋₉ alkyl)-OC(═O)—(C₃₋₈ alkyl) ester; and enzymatically converting the (C₄₋₉ alkyl)-OC(═O)—(C₃₋₈ alkyl) ester to any of (C₄₋₉ alkyl)-OC(═O)—(C₃₋₈ hydroxyalkyl) ester, (C₄₋₉ hydroxyalkyl)-OC(═O)—(C₃₋₈ hydroxyalkyl) ester, or (C₄₋₉ hydroxyalkyl)-OC(═O)—(C₃₋₈ alkyl) ester.

In some embodiments, the C₄₋₉ alkanoyl-CoA can be enzymatically converted to the (C₄₋₉ alkyl)-OC(═O)—(C₃₋₈ alkyl) ester using a polypeptide having alcohol O-acetyltransferase activity. In some embodiments, the alcohol O-acetyltransferase can have at least 70% sequence identity to the amino acid sequence set forth in SEQ ID NO: 26.

In some embodiments, the (C₄₋₉ alkyl)-OC(═O)—(C₃₋₈ alkyl) ester can be enzymatically converted to any of (C₄₋₉ alkyl)-OC(═O)—(C₃₋₈ hydroxyalkyl) ester, (C₄₋₉ hydroxyalkyl)-OC(═O)—(C₃₋₈ hydroxyalkyl) ester, or (C₄₋₉ hydroxyalkyl)-OC(═O)—(C₃₋₈ alkyl) ester using a polypeptide having monooxygenase activity. In some embodiments, the polypeptide having monooxygenase activity can be classified under EC 1.14.14.- or EC 1.14.15.-.

In some embodiments, the method further can include enzymatically converting the (C₄₋₉ hydroxyalkyl)-OC(═O)—(C₃₋₈ hydroxyalkyl) ester or (C₄₋₉ hydroxyalkyl)-OC(═O)—(C₃₋₈ alkyl) ester to a C₄₋₉ hydroxyalkanoate. In some embodiments, a polypeptide having esterase activity enzymatically converts the (C₄₋₉ hydroxyalkyl)-OC(═O)—(C₃₋₈ hydroxyalkyl) ester or (C₄₋₉ hydroxyalkyl)-OC(═O)—(C₃₋₈ alkyl) ester to the C₄₋₉ hydroxyalkanoate.

In one aspect, this document features a method for producing a bioderived 5-carbon compound. The method for producing a bioderived 5-carbon compound can include culturing or growing a recombinant host as described herein under conditions and for a sufficient period of time to produce the bioderived 5-carbon compound, wherein, optionally, the bioderived 5-carbon compound is selected from the group consisting of glutaric acid, glutarate semialdehyde, 5-aminopentanoate acid, 5-hydroxypentanoate, pentamethylenediamine, 1,5-pentanediol, and combinations thereof.

In one aspect, this document features composition comprising a bioderived 5-carbon compound as described herein and a compound other than the bioderived 5-carbon compound, wherein the bioderived 5-carbon compound is selected from the group consisting of glutaric acid, glutarate semialdehyde, 5-aminopentanoate acid, 5-hydroxypentanoate, pentamethylenediamine, 1,5-pentanediol, and combinations thereof. For example, the bioderived 5-carbon compound is a cellular portion of a host cell or an organism.

This document also features a biobased polymer comprising the bioderived glutaric acid, glutarate semialdehyde, 5-aminopentanoate acid, 5-hydroxypentanoate, pentamethylenediamine, 1,5-pentanediol, and combinations thereof.

This document also features a biobased resin comprising the bioderived glutaric acid, glutarate semialdehyde, 5-aminopentanoate acid, 5-hydroxypentanoate, pentamethylenediamine, 1,5-pentanediol, and combinations thereof. as well as a molded product obtained by molding a biobased resin.

In another aspect, this document features a process for producing a biobased polymer that includes chemically reacting the bioderived glutaric acid, glutarate semialdehyde, 5-aminopentanoate acid, 5-hydroxypentanoate, pentamethylenediamine, 1,5-pentanediol, and combinations thereof with itself or another compound in a polymer producing reaction.

In another aspect, this document features a process for producing a biobased resin that includes chemically reacting the bioderived glutaric acid, glutarate semialdehyde, 5-aminopentanoate acid, 5-hydroxypentanoate, pentamethylenediamine, 1,5-pentanediol, and combinations thereof with itself or another compound in a resin producing reaction.

In another aspect, this document provides a bio-derived product, bio-based product or fermentation-derived product, wherein said product comprises:

(i) a composition comprising at least one bio-derived, bio-based or fermentation-derived compound provided herein or in any one of FIGS. 1-9, or any combination thereof;

(ii) a bio-derived, bio-based or fermentation-derived polymer comprising the bio-derived, bio-based or fermentation-derived composition or compound of (i), or any combination thereof;

(iii) a bio-derived, bio-based or fermentation-derived resin comprising the bio-derived, bio-based or fermentation-derived compound or bio-derived, bio-based or fermentation-derived composition of (i) or any combination thereof or the bio-derived, bio-based or fermentation-derived polymer of (ii) or any combination thereof;

(iv) a molded substance obtained by molding the bio-derived, bio-based or fermentation-derived polymer of (ii) or the bio-derived, bio-based or fermentation-derived resin of (iii), or any combination thereof;

(v) a bio-derived, bio-based or fermentation-derived formulation comprising the bio-derived, bio-based or fermentation-derived composition of (i), bio-derived, bio-based or fermentation-derived compound of (i), bio-derived, bio-based or fermentation-derived polymer of (ii), bio-derived, bio-based or fermentation-derived resin of (iii), or bio-derived, bio-based or fermentation-derived molded substance of (iv), or any combination thereof; or

(vi) a bio-derived, bio-based or fermentation-derived semi-solid or a non-semi-solid stream, comprising the bio-derived, bio-based or fermentation-derived composition of (i), bio-derived, bio-based or fermentation-derived compound of (i), bio-derived, bio-based or fermentation-derived polymer of (ii), bio-derived, bio-based or fermentation-derived resin of (iii), bio-derived, bio-based or fermentation-derived formulation of (v), or bio-derived, bio-based or fermentation-derived molded substance of (iv), or any combination thereof.

Also, described herein is a biochemical network comprising at least one exogenous nucleic acid encoding a polypeptide having (i) fatty acid O-methyltransferase activity or alcohol O-acetyltransferase activity, (ii) monooxygenase activity, and (iii) esterase or demethylase activity.

Also, described herein is a biochemical network comprising at least one exogenous nucleic acid encoding a polypeptide having fatty acid O-methyltransferase activity and a polypeptide having monooxygenase activity, wherein the biochemical network enzymatically produces 5-hydroxypentanoate methyl ester. The biochemical network can further include a polypeptide having demethylase activity or a polypeptide having esterase activity, wherein the polypeptide having demethylase activity or a polypeptide having esterase activity enzymatically produce 5-hydroxypentanoate.

The biochemical network can further include at least one exogenous nucleic acid encoding a polypeptide having β-ketothiolase activity or a polypeptide having acetyl-CoA carboxylase activity and a polypeptide having β-ketoacyl-[acp] synthase activity, a polypeptide having 3-hydroxyacyl-CoA dehydrogenase activity or a polypeptide having 3-oxoacyl-CoA reductase activity, a polypeptide having enoyl-CoA hydratase activity, and a polypeptide having trans-2-enoyl-CoA reductase activity, wherein the polypeptide having β-ketothiolase activity or a polypeptide having acetyl-CoA carboxylase activity and a polypeptide having β-ketoacyl-[acp] synthase activity, a polypeptide having 3-hydroxyacyl-CoA dehydrogenase activity or a polypeptide having 3-oxoacyl-CoA reductase activity, a polypeptide having enoyl-CoA hydratase activity, and a polypeptide having trans-2-enoyl-CoA reductase activity enzymatically produce C5 precursor molecules such as pentanoyl-CoA.

The biochemical network can further one or more of an exogenous polypeptide having thioesterase activity, a polypeptide having aldehyde dehydrogenase activity, or a polypeptide having butanal dehydrogenase activity, wherein the polypeptide having thioesterase activity, a polypeptide having aldehyde dehydrogenase activity, or a polypeptide having butanal dehydrogenase activity enzymatically produce pentanoate as a C5 precursor molecule.

Also, described herein is a biochemical network comprising at least one exogenous nucleic acid encoding a polypeptide having alcohol O-acetyltransferase activity and a polypeptide having monooxygenase activity, wherein the biochemical network produces pentanoic acid pentyl ester. The biochemical network can further include an esterase, wherein the esterase enzymatically converts pentanoic acid pentyl ester to 5-hydroxypentanoate and/or 1,5-pentanediol.

The biochemical network can further include at least one exogenous nucleic acid encoding a polypeptide having β-ketothiolase activity or a polypeptide having acetyl-CoA carboxylase activity and a polypeptide having β-ketoacyl-[acp] synthase activity, a polypeptide having 3-hydroxyacyl-CoA dehydrogenase activity or a polypeptide having 3-oxoacyl-CoA reductase activity, a polypeptide having enoyl-CoA hydratase activity, and a polypeptide having trans-2-enoyl-CoA reductase activity, wherein the polypeptide having β-ketothiolase activity or a polypeptide having acetyl-CoA carboxylase activity and a polypeptide having β-ketoacyl-[acp] synthase activity, a polypeptide having 3-hydroxyacyl-CoA dehydrogenase activity or a polypeptide having 3-oxoacyl-CoA reductase activity, a polypeptide having enoyl-CoA hydratase activity, and a polypeptide having trans-2-enoyl-CoA reductase activity enzymatically produce C5 precursor molecules such as pentanoyl-CoA. The biochemical network can further include one or more of an exogenous a polypeptide having aldehyde dehydrogenase activity, a polypeptide having alcohol dehydrogenase activity, a polypeptide having butanal dehydrogenase activity, a polypeptide having carboxylate reductase activity or a polypeptide having thioesterase activity, wherein the polypeptide having aldehyde dehydrogenase activity, a polypeptide having alcohol dehydrogenase activity, a polypeptide having butanal dehydrogenase activity, a polypeptide having carboxylate reductase activity or a polypeptide having thioesterase activity enzymatically produce pentanol as a C5 precursor molecule.

A biochemical network producing 5-hydroxypentanoate can further include one or more of a polypeptide having monooxygenase activity, a polypeptide having alcohol dehydrogenase activity, a polypeptide having aldehyde dehydrogenase activity, a polypeptide having 7-oxohexanoate dehydrogenase activity, a polypeptide having 6-oxohexanoate dehydrogenase activity, a polypeptide having 5-hydroxypentanoate dehydrogenase activity, a polypeptide having 4-hydroxybutyrate dehydrogenase activity or a polypeptide having 6-hydroxyhexanoate dehydrogenase activity, wherein the polypeptide having monooxygenase activity, a polypeptide having alcohol dehydrogenase activity, a polypeptide having aldehyde dehydrogenase activity, a polypeptide having 7-oxohexanoate dehydrogenase activity, a polypeptide having 6-oxohexanoate dehydrogenase activity, a polypeptide having 5-hydroxypentanoate dehydrogenase activity, a polypeptide having 4-hydroxybutyrate dehydrogenase activity or a polypeptide having 6-hydroxyhexanoate dehydrogenase activity enzymatically convert 5-hydroxyheptanoate to glutaric acid or glutarate semialdehyde.

A biochemical network producing 5-hydroxypentanoate can further include one or more of a polypeptide having ω-transaminase activity, a polypeptide having 6-hydroxyhexanoate dehydrogenase activity, a polypeptide having 5-hydroxybutanoate dehydrogenase activity, a polypeptide having 4-hydroxybutyrate dehydrogenase activity and a polypeptide having alcohol dehydrogenase activity, wherein the polypeptide having ω-transaminase activity, a polypeptide having 6-hydroxyhexanoate dehydrogenase activity, a polypeptide having 5-hydroxybutanoate dehydrogenase activity, a polypeptide having 4-hydroxybutyrate dehydrogenase activity and a polypeptide having alcohol dehydrogenase activity enzymatically convert 5-hydroxypentanoate to 5-aminopentanoate.

A biochemical network producing 5-aminopentanoate, 5-hydroxypentanoate, glutarate semialdehyde, or 1,5-pentanediol can further include one or more of a polypeptide having carboxylate reductase activity, a polypeptide having ω-transaminase activity, a polypeptide having deacetylase activity, a polypeptide having N-acetyl transferase activity, or a polypeptide having alcohol dehydrogenase activity, wherein the a polypeptide having carboxylate reductase activity, a polypeptide having ω-transaminase activity, a polypeptide having deacetylase activity, a polypeptide having N-acetyl transferase activity, or a polypeptide having alcohol dehydrogenase activity, enzymatically convert 5-aminopentanoate, 5-hydroxypentanoate, glutarate semialdehyde, or 1,5-pentanediol to cadaverine.

A biochemical network producing 5-hydroxypentanoate can further include one or more of a polypeptide having carboxylate reductase activity and a polypeptide having alcohol dehydrogenase activity, wherein the polypeptide having carboxylate reductase activity and a polypeptide having alcohol dehydrogenase activity enzymatically convert 5-hydroxypentanoate to 1,5-pentanediol.

Also, described herein is a means for obtaining 5-hydroxypentanoate using (i) a polypeptide having fatty acid O-methyltransferase activity and a polypeptide having monooxygenase activity and (ii) a polypeptide having demethylase activity or a polypeptide having esterase activity. The means can further include means for converting 5-hydroxypentanoate to at least one of glutaric acid, 5-aminopentanoate, cadaverine, 5-hydroxypentanoate, and 1,5-pentanediol. The means can include a polypeptide having aldehyde dehydrogenase activity, a polypeptide having 7-oxohexanoate dehydrogenase activity, a polypeptide having 6-oxohexanoate dehydrogenase activity, a polypeptide having 5-hydroxypentanoate dehydrogenase activity, a polypeptide having 4-hydroxybutyrate dehydrogenase activity or a polypeptide having 6-hydroxyhexanoate dehydrogenase activity.

Also, described herein is a means for obtaining 5-hydroxypentanoate using (i) a polypeptide having alcohol O-acetyltransferase and a polypeptide having monooxygenase activity and (ii) a polypeptide having demethylase activity or a polypeptide having esterase activity. The means can further include means for converting 5-hydroxypentanoate to at least one of glutaric acid, 5-aminopentanoate, cadaverine, 5-hydroxypentanoate, and 1,5-pentanediol. The means can include a polypeptide having aldehyde dehydrogenase activity, a polypeptide having 7-oxohexanoate dehydrogenase activity, a polypeptide having 6-oxohexanoate dehydrogenase activity, a polypeptide having 5-hydroxypentanoate dehydrogenase activity, a polypeptide having 4-hydroxybutyrate dehydrogenase activity or a polypeptide having 6-hydroxyhexanoate dehydrogenase activity.

Also described herein is (i) a step for obtaining 5-hydroxypentanoate using a polypeptide having alcohol O-acetyltransferase, a polypeptide having monooxygenase activity, and a polypeptide having demethylase activity or a polypeptide having esterase activity, and (ii) a step for obtaining glutaric acid, 5-aminopentanoate, glutarate semialdehyde 1,5-pentanediol, or cadaverine using a polypeptide having carboxylate reductase activity, a polypeptide having alcohol dehydrogenase activity, a polypeptide having ω-transaminase activity, a polypeptide having deacetylase activity, a polypeptide having N-acetyl transferase activity, a polypeptide having 6-hydroxyhexanoate dehydrogenase activity, a polypeptide having 5-hydroxybutanoate dehydrogenase activity, a polypeptide having 4-hydroxybutyrate dehydrogenase activity, a polypeptide having aldehyde dehydrogenase activity, a polypeptide having 7-oxohexanoate dehydrogenase activity, a polypeptide having 6-oxohexanoate dehydrogenase activity, a polypeptide having 5-hydroxypentanoate dehydrogenase activity, a polypeptide having 4-hydroxybutyrate dehydrogenase activity or a polypeptide having 6-hydroxyhexanoate dehydrogenase activity,

In another aspect, this document features a composition comprising 5-hydroxypentanoate and a polypeptide having alcohol O-acetyltransferase, a polypeptide having monooxygenase activity, and a polypeptide having demethylase activity or a polypeptide having esterase activity complex. The composition can be cellular. The composition can further include a polypeptide having carboxylate reductase activity, a polypeptide having alcohol dehydrogenase activity, a polypeptide having ω-transaminase activity, a polypeptide having deacetylase activity, a polypeptide having N-acetyl transferase activity, a polypeptide having 6-hydroxyhexanoate dehydrogenase activity, a polypeptide having 5-hydroxybutanoate dehydrogenase activity, a polypeptide having 4-hydroxybutyrate dehydrogenase activity, a polypeptide having aldehyde dehydrogenase activity, a polypeptide having 7-oxohexanoate dehydrogenase activity, a polypeptide having 6-oxohexanoate dehydrogenase activity, a polypeptide having 5-hydroxypentanoate dehydrogenase activity, a polypeptide having 4-hydroxybutyrate dehydrogenase activity or a polypeptide having 6-hydroxyhexanoate dehydrogenase activity, and at least one of glutaric acid, 5-aminopentanoic acid, cadaverine, 5-hydroxypentanoate, and 1,5-pentanediol. The composition can be cellular.

The reactions of the pathways described herein can be performed in one or more cell (e.g., host cell) strains (a) naturally expressing one or more relevant enzymes, (b) genetically engineered to express one or more relevant enzymes, or (c) naturally expressing one or more relevant enzymes and genetically engineered to express one or more relevant enzymes. Alternatively, relevant enzymes can be extracted from of the above types of host cells and used in a purified or semi-purified form. Extracted enzymes can optionally be immobilized to the floors and/or walls of appropriate reaction vessels. Moreover, such extracts include lysates (e.g. cell lysates) that can be used as sources of relevant enzymes. In the methods provided by the document, all the steps can be performed in cells (e.g., host cells), all the steps can be performed using extracted enzymes, or some of the steps can be performed in cells and others can be performed using extracted enzymes.

Unless otherwise defined, all technical and scientific terms used herein have the same meaning as commonly understood by one of ordinary skill in the art to which this invention pertains. Although methods and materials similar or equivalent to those described herein can be used to practice the invention, suitable methods and materials are described below. All publications, patent applications, patents, and other references mentioned herein including GenBank and NCBI submissions with accession numbers are incorporated by reference in their entirety. In case of conflict, the present specification, including definitions, will control. In addition, the materials, methods, and examples are illustrative only and not intended to be limiting.

The details of one or more embodiments of the invention are set forth in the accompanying drawings and the description below. Other features, objects, and advantages of the invention will be apparent from the description and the drawings, and from the claims. The word “comprising” in the claims may be replaced by “consisting essentially of” or with “consisting of,” according to standard practice in patent law.

DESCRIPTION OF DRAWINGS

FIG. 1 is a schematic of exemplary biochemical pathways leading to pentanoyl-CoA using NADH-dependent enzymes and acetyl-CoA and propanoyl-CoA as central metabolites.

FIG. 2 is a schematic of exemplary biochemical pathways leading to pentanoyl-CoA using NADPH-dependent enzymes and with acetyl-CoA and propanoyl-CoA as central metabolites.

FIG. 3 is a schematic of exemplary biochemical pathways leading to pentanoate and pentanol using pentanoyl-CoA as a central precursor.

FIG. 4 is a schematic of an exemplary biochemical pathway leading to glutaric acid using 5-hydroxypentanoate as a central precursor.

FIG. 5 is a schematic of an exemplary biochemical pathway leading to 5-aminopentanoate using 5-hydroxypentanoate as a central precursor.

FIG. 6 is a schematic of exemplary biochemical pathways leading to cadaverine using 5-aminopentanoate, 5-hydroxypentanoate, glutarate semialdehyde (also known as 5-oxopentanoic acid), or 1,5-pentanediol as a central precursor.

FIG. 7 is a schematic of exemplary biochemical pathways leading to 5-hydroxypentanoate via ester intermediates using pentanoate or pentanoyl-CoA. FIG. 7 also contains an exemplary biochemical pathway leading to 5-hydroxypentanoate using 1,5-pentanediol as a central precursor.

FIG. 8 is a schematic of exemplary biochemical pathways leading to 1,5 pentanediol using 5-hydroxypentanoate or pentanoyl-CoA as a central precursor.

FIG. 9 is a schematic of exemplary biochemical pathways leading to propanoyl-CoA from central metabolites.

FIG. 10 contains the amino acid sequences of an Escherichia coli thioesterase encoded by tesB (see GenBank Accession No. AAA24665.1, SEQ ID NO: 1), a Mycobacterium marinum carboxylate reductase (see Genbank Accession No. ACC40567.1, SEQ ID NO: 2), a Mycobacterium smegmatis carboxylate reductase (see Genbank Accession No. ABK71854.1, SEQ ID NO: 3), a Segniliparus rugosus carboxylate reductase (see Genbank Accession No. EFV11917.1, SEQ ID NO: 4), a Mycobacterium smegmatis carboxylate reductase (see Genbank Accession No. ABK75684.1, SEQ ID NO: 5), a Mycobacterium massiliense carboxylate reductase (see Genbank Accession No. EIV11143.1, SEQ ID NO: 6), a Segniliparus rotundus carboxylate reductase (see Genbank Accession No. ADG98140.1, SEQ ID NO: 7), a Chromobacterium violaceum ω-transaminase (see Genbank Accession No. AAQ59697.1, SEQ ID NO: 8), a Pseudomonas aeruginosa ω-transaminase (see Genbank Accession No. AAG08191.1, SEQ ID NO: 9), a Pseudomonas syringae ω-transaminase (see Genbank Accession No. AAY39893.1, SEQ ID NO: 10), a Rhodobacter sphaeroides ω-transaminase (see Genbank Accession No. ABA81135.1, SEQ ID NO: 11), an Escherichia coli ω-transaminase (see Genbank Accession No. AAA57874.1, SEQ ID NO: 12), a Vibrio fluvialis ω-transaminase (See Genbank Accession No. AEA39183.1, SEQ ID NO: 13); a Polaromonas sp. JS666 monooxygenase (see Genbank Accession No. ABE47160.1, SEQ ID NO:14), a Mycobacterium sp. HXN-1500 monooxygenase (see Genbank Accession No. CAH04396.1, SEQ ID NO:15), a Mycobacterium austroafricanum monooxygenase (see Genbank Accession No. ACJ06772.1, SEQ ID NO:16), a Polaromonas sp. JS666 oxidoreductase (see Genbank Accession No. ABE47159.1, SEQ ID NO:17), a Mycobacterium sp. HXN-1500 oxidoreductase (see Genbank Accession No. CAH04397.1, SEQ ID NO:18), a Polaromonas sp. JS666 ferredoxin (see Genbank Accession No. ABE47158.1, SEQ ID NO:19), a Mycobacterium sp. HXN-1500 ferredoxin (see Genbank Accession No. CAH04398.1, SEQ ID NO:20), Bacillus subtilis phosphopantetheinyl transferase (see Genbank Accession No. CAA44858.1, SEQ ID NO:21), a Nocardia sp. NRRL 5646 phosphopantetheinyl transferase (see Genbank Accession No. ABI83656.1, SEQ ID NO:22), a Mycobacterium marinum fatty acid O-methyltransferase (GenBank Accession No. ACC41782.1; SEQ ID NO:23), a Mycobacterium smegmatis str. MC2 fatty acid O-methyltransferase (GenBank Accession No. ABK73223.1; SEQ ID NO:24), a Pseudomonas putida fatty acid O-methyltransferase (GenBank Accession No. CAA39234.1; SEQ ID NO:25), a Saccharomyces cerevisiae alcohol O-acetyltransferase (Genbank Accession No: CAA85138.1, SEQ ID NO: 26), a Pseudomonas fluorescens carboxylesterase (Genbank Accession No. AAC60471.2, SEQ ID NO: 27), a Pseudomonas putida alkane 1-monooxygenase (Genbank Accession No. CAB51047.1, SEQ ID NO: 28), a Candida maltose cytochrome P450 (Genbank Accession No: BAA00371.1, SEQ ID NOs: 29), a Salmonella enterica subsp. enterica serovar Typhimurium butanal dehydrogenase (GenBank Accession No. AAD39015, SEQ ID NO:30), a Sphingomonas paucimobilis demethylase (GenBank Accession No. BAD61059.1 and GenBank Accession No. BAC59257.1, SEQ ID NOs: 31 and 32, respectively), a Lactobacillus brevis thioesterase (GenBank Accession No. ABJ63754.1, SEQ ID NO:33), and a Lactobacillus plantarum thioesterase (GenBank Accession No. CCC58182.1, SEQ ID NO:34).

FIG. 11 is a bar graph of the change in absorbance at 340 nm after 20 min, which is a measure of the consumption of NADPH and activity of carboxylate reductases for converting pentanoic acid to pentanal relative to the empty vector control.

FIG. 12 is a bar graph summarizing the change in absorbance at 340 nm after 20 minutes, which is a measure of the consumption of NADPH and activity of five carboxylate reductase preparations in enzyme only controls (no substrate).

FIG. 13 is a bar graph of the percent conversion after 4 hours of pyruvate to L-alanine (mol/mol) as a measure of the ω-transaminase activity of six ω-transaminase preparations for converting 5-aminopentanol to 5-oxopentanol relative to the empty vector control.

FIG. 14 is a bar graph of the change in absorbance at 340 nm after 20 minutes, which is a measure of the consumption of NADPH and the activity of five carboxylate reductase preparations for converting 5-hydroxypentanoate to 5-hydroxypentanal relative to the empty vector control.

FIG. 15 is a bar graph of the percent conversion after 4 hours of pyruvate to L-alanine (mol/mol) as a measure of the ω-transaminase activity of five ω-transaminase preparations for converting N5-acetyl-1,5-diaminopentane to N5-acetyl-5-aminopentanal relative to the empty vector control.

FIG. 16 is a bar graph of the change in absorbance at 340 nm after 20 minutes, which is a measure of the consumption of NADPH and activity of a carboxylate reductase preparation for converting glutarate semialdehyde to pentanedial relative to the empty vector control.

FIG. 17 is a bar graph summarizing the percent conversion of pyruvate to L-alanine (mol/mol) as a measure of the ω-transaminase activity of the enzyme only controls (no substrate).

FIG. 18 is a bar graph of the percent conversion after 4 hours of pyruvate to L-alanine (mol/mol) as a measure of the ω-transaminase activity of one ω-transaminase preparation for converting 5-aminopentanoate to glutarate semialdehyde relative to the empty vector control.

FIG. 19 is a bar graph of the percent conversion after 4 hours of L-alanine to pyruvate (mol/mol) as a measure of the ω-transaminase activity of one ω-transaminase preparation for converting glutarate semialdehyde to 5-aminopentanoate relative to the empty vector control.

FIG. 20 is a bar graph of the percent conversion after 4 hours of pyruvate to L-alanine (mol/mol) as a measure of the ω-transaminase activity of four ω-transaminase preparations for converting cadaverine to 5-aminopentanal relative to the empty vector control.

DETAILED DESCRIPTION

This document provides enzymes, non-natural pathways, cultivation strategies, feedstocks, central precursors, host microorganisms and attenuations to the host's biochemical network, which generate a seven carbon chain aliphatic backbone (which can be bound to a coenzyme A moiety) from central metabolites in which one or two terminal functional groups may be formed leading to the synthesis of one or more of glutaric acid, 5-hydroxypentanoate, 5-aminopentanoate, cadaverine or 1,5-pentanediol (referred to as “C5 building blocks” herein). As used herein, the term “central precursor” is used to denote any metabolite in any metabolic pathway shown herein leading to the synthesis of a C5 building block. The term “central metabolite” is used herein to denote a metabolite that is produced in all microorganisms to support growth.

Host microorganisms described herein can include endogenous pathways that can be manipulated such that one or more C5 building blocks or central precursors thereof can be produced. In an endogenous pathway, the host microorganism naturally expresses all of the enzymes catalyzing the reactions within the pathway. A host microorganism containing an engineered pathway does not naturally express all of the enzymes catalyzing the reactions within the pathway but has been engineered such that all of the enzymes within the pathway are expressed in the host.

The term “exogenous” as used herein with reference to a nucleic acid (or a protein) and a host refers to a nucleic acid that does not occur in (and cannot be obtained from) a cell of that particular type as it is found in nature or a protein encoded by such a nucleic acid. Thus, a non-naturally-occurring nucleic acid is considered to be exogenous to a host once in the host. It is important to note that non-naturally-occurring nucleic acids can contain nucleic acid subsequences or fragments of nucleic acid sequences that are found in nature provided the nucleic acid as a whole does not exist in nature. For example, a nucleic acid molecule containing a genomic DNA sequence within an expression vector is non-naturally-occurring nucleic acid, and thus is exogenous to a host cell once introduced into the host, since that nucleic acid molecule as a whole (genomic DNA plus vector DNA) does not exist in nature. Thus, any vector, autonomously replicating plasmid, or virus (e.g., retrovirus, adenovirus, or herpes virus) that as a whole does not exist in nature is considered to be non-naturally-occurring nucleic acid. It follows that genomic DNA fragments produced by PCR or restriction endonuclease treatment as well as cDNAs are considered to be non-naturally-occurring nucleic acid since they exist as separate molecules not found in nature. It also follows that any nucleic acid containing a promoter sequence and polypeptide-encoding sequence (e.g., cDNA or genomic DNA) in an arrangement not found in nature is non-naturally-occurring nucleic acid. A nucleic acid that is naturally-occurring can be exogenous to a particular host microorganism. For example, an entire chromosome isolated from a cell of yeast x is an exogenous nucleic acid with respect to a cell of yeast y once that chromosome is introduced into a cell of yeast y.

In contrast, the term “endogenous” as used herein with reference to a nucleic acid (e.g., a gene) (or a protein) and a host refers to a nucleic acid (or protein) that does occur in (and can be obtained from) that particular host as it is found in nature. Moreover, a cell “endogenously expressing” a nucleic acid (or protein) expresses that nucleic acid (or protein) as does a host of the same particular type as it is found in nature. Moreover, a host “endogenously producing” or that “endogenously produces” a nucleic acid, protein, or other compound produces that nucleic acid, protein, or compound as does a host of the same particular type as it is found in nature.

For example, depending on the host and the compounds produced by the host, one or more of the following polypeptides may be expressed in the host in addition to a polypeptide having fatty acid O-methyltransferase activity or a polypeptide having alcohol O-acetyltransferase activity: a monooxygenase, an esterase, a demethylase, a β-ketothiolase, an acetyl-CoA carboxylase, a β-ketoacyl-[acp] synthase, a 3-hydroxyacyl-CoA dehydrogenase, a 3-oxoacyl-CoA reductase, an enoyl-CoA hydratase, a trans-2-enoyl-CoA reductase, a thioesterase, an aldehyde dehydrogenase, a butanal dehydrogenase, a monooxygenase in, for example, the CYP4F3B family, an alcohol dehydrogenase, a 7-oxoheptanoate dehydrogenase, a 6-oxohexanoate dehydrogenase, a 5-oxopentanoate dehydrogenase, a ω-transaminase, a 6-hydroxyhexanoate dehydrogenase, a 5-hydroxypentanoate dehydrogenase, 4-hydroxybutyrate dehydrogenase, a carboxylate reductase, a deacetylase, or an N-acetyl transferase. In recombinant hosts expressing a carboxylate reductase, a phosphopantetheinyl transferase also can be expressed as it enhances activity of the carboxylate reductase. In recombinant hosts expressing a monooxygenase, an electron transfer chain protein such as an oxidoreductase and/or ferredoxin polypeptide also can be expressed.

In some embodiments, a recombinant host can include at least one exogenous nucleic acid encoding a polypeptide having (i) fatty acid O-methyltransferase activity or alcohol O-acetyltransferase activity, (ii) monooxygenase activity, and (iii) esterase or demethylase activity.

In some embodiments, a recombinant host can include at least one exogenous nucleic acid encoding a polypeptide having fatty acid O-methyltransferase and a polypeptide having monooxygenase activity, wherein the host produces 5-hydroxypentanoate methyl ester. Such a host further can include a polypeptide having demethylase or esterase activity and further produce 5-hydroxypentanoate. In some embodiments, the recombinant host also can include at least one exogenous nucleic acid encoding a polypeptide having β-ketothiolase activity or a polypeptide having acetyl-CoA carboxylase activity and a polypeptide having β-ketoacyl-[acp] synthase activity, a polypeptide having 3-hydroxyacyl-CoA dehydrogenase activity or a polypeptide having 3-oxoacyl-CoA reductase activity, a polypeptide having enoyl-CoA hydratase activity, and a polypeptide having trans-2-enoyl-CoA reductase activity to produce C5 precursor molecules such as pentanoyl-CoA. Such a host further can include one or more of (e.g., two or three of) an exogenous polypeptide having thioesterase activity, a polypeptide having aldehyde dehydrogenase activity, or a polypeptide having butanal dehydrogenase activity, and produce pentanoate as a C5 precursor molecule.

In some embodiments, a recombinant host can include at least one exogenous nucleic acid encoding a polypeptide having alcohol O-acetyltransferase activity and a polypeptide having monooxygenase activity, wherein the host produces pentanoic acid pentyl ester. Such a host further can include a polypeptide having esterase activity and further produce 5-hydroxypentanoate and/or 1,5-pentanediol. In some embodiments, the recombinant host also can include at least one exogenous nucleic acid encoding a polypeptide having β-ketothiolase activity or a polypeptide having acetyl-CoA carboxylase activity and a polypeptide having β-ketoacyl-[acp] synthase activity, a polypeptide having 3-hydroxyacyl-CoA dehydrogenase activity or a polypeptide having 3-oxoacyl-CoA reductase activity, a polypeptide having enoyl-CoA hydratase activity, and a polypeptide having trans-2-enoyl-CoA reductase activity to produce C5 precursor molecules such as pentanoyl-CoA. Such a host further can include one or more of (e.g., two or three of) an exogenous polypeptide having aldehyde dehydrogenase activity, a polypeptide having alcohol dehydrogenase activity, a polypeptide having butanal dehydrogenase activity, a polypeptide having carboxylate reductase activity or a polypeptide having thioesterase activity and produce pentanol as a C5 precursor molecule.

A recombinant host producing 5-hydroxypentanoate further can include one or more polypeptides having an activity of a monooxygenase (e.g., in the CYP4F3B family) an alcohol dehydrogenase, an aldehyde dehydrogenase, a 6-hydroxyhexanoate dehydrogenase, a 7-oxoheptanoate dehydrogenase, a 6-oxohexanoate dehydrogenase, a 5-hydroxypentanoate dehydrogenase, a 4-hydroxybutyrate dehydrogenase or a 5-oxopentanoate dehydrogenase, and produce glutaric acid. For example, a recombinant host further can include a polypeptide having monooxygenase activity and produce glutaric acid. As another example, a recombinant host further can include a polypeptide having the activity of (i) an alcohol dehydrogenase, a 6-hydroxyhexanoate dehydrogenase, a 5-hydroxypentanoate dehydrogenase, or a 4-hydroxybutyrate dehydrogenase or (ii) an aldehyde dehydrogenase, a 7-oxoheptanoate dehydrogenase, a 6-oxohexanoate dehydrogenase, or a 5-oxopentanoate dehydrogenase, and produce glutaric acid.

A recombinant host producing 5-hydroxypentanoate further can include one or more polypeptides having the activity of a transaminase, a 6-hydroxyhexanoate dehydrogenase, a 5-hydroxypentanoate dehydrogenase, a 4-hydroxybutyrate dehydrogenase and an alcohol dehydrogenase, and produce 5-aminopentanoate. For example, a recombinant host producing 5-hydroxypentanoate further can include a polypeptide having ω-transaminase activity and either a polypeptide having 6-hydroxyhexanoate dehydrogenase activity or having alcohol dehydrogenase activity.

A recombinant host producing 5-aminopentanoate, 5-hydroxypentanoate, glutarate semialdehyde or 1,5-pentanediol further can include one or more of a polypeptide having carboxylate reductase activity, a polypeptide having ω-transaminase activity, a polypeptide having deacetylase activity, a polypeptide having N-acetyl transferase activity, or a polypeptide having alcohol dehydrogenase activity, and produce cadaverine. In some embodiments, a recombinant host further can include each of a polypeptide having carboxylate reductase activity, a polypeptide having ω-transaminase activity, a polypeptide having deacetylase activity, and a polypeptide having N-acetyl transferase activity. In some embodiments, a recombinant host further can include a polypeptide having carboxylate reductase activity and a polypeptide having ω-transaminase activity. In some embodiments, a recombinant host further can include a polypeptide having carboxylate reductase activity, a polypeptide having ω-transaminase activity, and a polypeptide having alcohol dehydrogenase activity. In the embodiments in which the recombinant host produces 5-aminopentanoate, an additional ω-transaminase may not be necessary to produce cadaverine. In some embodiments, the host includes a second exogenous polypeptide having ω-transaminase activity that differs from the first exogenous polypeptide having ω-transaminase activity.

A recombinant host producing 5-hydroxypentanoic acid further can include one or more of a polypeptide having carboxylate reductase activity and a polypeptide having alcohol dehydrogenase activity, and produce 1,5-pentanediol.

Within an engineered pathway, the enzymes can be from a single source, i.e., 5 from one species or genus, or can be from multiple sources, i.e., different species or genera. Nucleic acids encoding the enzymes described herein have been identified from various organisms and are readily available in publicly available databases such as GenBank or EMBL. In recombinant hosts containing an exogenous enzyme, the hosts contain an exogenous nucleic acid encoding the enzyme.

Any of the enzymes described herein that can be used for production of one or more C5 building blocks can have at least 70% sequence identity (homology) (e.g., at least 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100%) to the amino acid sequence of the corresponding wild-type enzyme. It will be appreciated that the sequence identity can be determined on the basis of the mature enzyme (e.g., with any signal sequence removed) or on the basis of the immature enzyme (e.g., with any signal sequence included). It also will be appreciated that the initial methionine residue may or may not be present on any of the enzyme sequences described herein.

For example, a polypeptide having thioesterase activity described herein can have at least 70% sequence identity (homology) (e.g., at least 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100%) to the amino acid sequence of an Escherichia coli thioesterase encoded by tesB (see GenBank Accession No. AAA24665.1, SEQ ID NO: 1), to the amino acid sequence of a Lactobacillus brevis thioesterase (GenBank Accession No. ABJ63754.1, SEQ ID NO:33) or a Lactobacillus plantarum thioesterase (GenBank Accession No. CCC58182.1, SEQ ID NO:34). See FIG. 10.

For example, a polypeptide having carboxylate reductase activity described herein can have at least 70% sequence identity (homology) (e.g., at least 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100%) to the amino acid sequence of a Mycobacterium marinum (see Genbank Accession No. ACC40567.1, SEQ ID NO: 2), a Mycobacterium smegmatis (see Genbank Accession No. ABK71854.1, SEQ ID NO: 3), a Segniliparus rugosus (see Genbank Accession No. EFV11917.1, SEQ ID NO: 4), a Mycobacterium smegmatis (see Genbank Accession No. ABK75684.1, SEQ ID NO: 5), a Mycobacterium massiliense (see Genbank Accession No. EIV11143.1, SEQ ID NO: 6), or a Segniliparus rotundus (see Genbank Accession No. ADG98140.1, SEQ ID NO: 7) carboxylate reductase. See, FIG. 10.

For example, a polypeptide having ω-transaminase activity described herein can have at least 70% sequence identity (homology) (e.g., at least 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100%) to the amino acid sequence of a Chromobacterium violaceum (see Genbank Accession No. AAQ59697.1, SEQ ID NO: 8), a Pseudomonas aeruginosa (see Genbank Accession No. AAG08191.1, SEQ ID NO: 9), a Pseudomonas syringae (see Genbank Accession No. AAY39893.1, SEQ ID NO: 10), a Rhodobacter sphaeroides (see Genbank Accession No. ABA81135.1, SEQ ID NO: 11), an Escherichia coli (see Genbank Accession No. AAA57874.1, SEQ ID NO: 12), or a Vibrio fluvialis (see Genbank Accession No. AEA39183.1, SEQ ID NO: 13) ω-transaminase. Some of these ω-transaminases are diamine ω-transaminases. See, FIG. 10.

For example, a polypeptide having monooxygenase activity described herein can have at least 70% sequence identity (homology) (e.g., at least 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100%) to the amino acid sequence of a Polaromonas sp. JS666 monooxygenase (see Genbank Accession No. ABE47160.1, SEQ ID NO: 14), a Mycobacterium sp. HXN-1500 monooxygenase (see Genbank Accession No. CAH04396.1, SEQ ID NO:15), or a Mycobacterium austroafricanum monooxygenase (See Genbank Accession No. ACJ06772.1, SEQ ID NO:16). See, FIG. 10.

For example, a polypeptide having oxidoreductase activity described herein can have at least 70% sequence identity (homology) (e.g., at least 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100%) to the amino acid sequence of a Polaromonas sp. JS666 oxidoreductase (see Genbank Accession No. ABE47159.1, SEQ ID NO: 17) or a Mycobacterium sp. HXN-1500 oxidoreductase (see Genbank Accession No. CAH04397.1, SEQ ID NO: 18). See, FIG. 10.

For example, a polypeptide having ferredoxin activity described herein can have at least 70% sequence identity (homology) (e.g., at least 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100%) to the amino acid sequence of a Polaromonas sp. JS666 ferredoxin (see Genbank Accession No. ABE47158.1, SEQ ID NO: 19) or a Mycobacterium sp. HXN-1500 ferredoxin (see Genbank Accession No. CAH04398.1, SEQ ID NO: 20). See, FIG. 10.

For example, a polypeptide having phosphopantetheinyl transferase activity described herein can have at least 70% sequence identity (homology) (e.g., at least 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100%) to the amino acid sequence of a Bacillus subtilis phosphopantetheinyl transferase (see Genbank Accession No. CAA44858.1, SEQ ID NO: 21) or a Nocardia sp. NRRL 5646 phosphopantetheinyl transferase (see Genbank Accession No. ABI83656.1, SEQ ID NO: 22). See FIG. 10.

For example, a polypeptide having fatty acid O-methyltransferase activity described herein can have at least 70% sequence identity (homology) (e.g., at least 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100%) to the amino acid sequence of a Mycobacterium marinum (see GenBank Accession No. ACC41782.1, SEQ ID NO: 23), a Mycobacterium smegmatis (see GenBank Accession No. ABK73223.1, SEQ ID NO: 24), or a Pseudomonas putida (see GenBank Accession No. CAA39234.1, SEQ ID NO: 25) methyltransferase. See FIG. 10.

For example, a polypeptide having alcohol O-acetyltransferase activity described herein can have at least 70% sequence identity (homology) (e.g., at least 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100%) to the amino acid sequence of a Saccharomyces cerevisiae (see GenBank Accession No. CAA85138.1, SEQ ID NO: 26) alcohol O-acetyltransferase. See FIG. 10.

For example, a polypeptide having esterase activity described herein can have at least 70% sequence identity (homology) (e.g., at least 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100%) to the amino acid sequence of a Pseudomonas fluorescens (see GenBank Accession No. AAC60471.2, SEQ ID NO: 27) esterase. See FIG. 10.

For example, a polypeptide having alkane 1-monooxygenase activity described herein can have at least 70% sequence identity (homology) (e.g., at least 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100%) to the amino acid sequence of a Pseudomonas putida alkane 1-monooxygenase (see Genbank Accession No. CAB51047.1, SEQ ID NO: 28).

For example, a polypeptide having cytochrome P450 monooxygenase activity described herein can have at least 70% sequence identity (homology) (e.g., at least 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100%) to the amino acid sequence of a Candida maltose cytochrome P450 (see Genbank Accession No: BAA00371.1, SEQ ID NOs: 29).

For example, a polypeptide having butanal dehydrogenase activity described herein can have at least 70% sequence identity (homology) (e.g., at least 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100%) to the amino acid sequence of a Salmonella enterica subsp. enterica serovar Typhimurium butanal dehydrogenase (see GenBank Accession No. AAD39015, SEQ ID NO:30).

For example, a polypeptide having syringate O-demethylase activity described herein can have at least 70% sequence identity (homology) (e.g., at least 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100%) to the amino acid sequence of a Sphingomonas paucimobilis demethylase (see, GenBank Accession No. BAD61059.1 and GenBank Accession No. BAC59257.1, SEQ ID NOs: 31 and 32, respectively).

The percent identity (homology) between two amino acid sequences can be determined as follows. First, the amino acid sequences are aligned using the BLAST 2 Sequences (Bl2seq) program from the stand-alone version of BLASTZ containing BLASTP version 2.0.14. This stand-alone version of BLASTZ can be obtained from Fish & Richardson's web site (e.g., www.fr.com/blast/) or the U.S. government's National Center for Biotechnology Information web site (www.ncbi.nlm.nih.gov). Instructions explaining how to use the Bl2seq program can be found in the readme file accompanying BLASTZ. Bl2seq performs a comparison between two amino acid sequences using the BLASTP algorithm. To compare two amino acid sequences, the options of Bl2seq are set as follows: -i is set to a file containing the first amino acid sequence to be compared (e.g., C:\seq1.txt); -j is set to a file containing the second amino acid sequence to be 5 compared (e.g., C:\seq2.txt); -p is set to blastp; -o is set to any desired file name (e.g., C:\output.txt); and all other options are left at their default setting. For example, the following command can be used to generate an output file containing a comparison between two amino acid sequences: C:\Bl2seq -i c:\seq1.txt -j c:\seq2.txt -p blastp -o c:\output.txt. If the two compared sequences share homology (identity), then the designated output file will present those regions of homology as aligned sequences. If the two compared sequences do not share homology (identity), then the designated output file will not present aligned sequences. Similar procedures can be following for nucleic acid sequences except that blastn is used.

Once aligned, the number of matches is determined by counting the number of positions where an identical amino acid residue is presented in both sequences. The percent identity (homology) is determined by dividing the number of matches by the length of the full-length polypeptide amino acid sequence followed by multiplying the resulting value by 100. It is noted that the percent identity (homology) value is rounded to the nearest tenth. For example, 78.11, 78.12, 78.13, and 78.14 is rounded down to 78.1, while 78.15, 78.16, 78.17, 78.18, and 78.19 is rounded up to 78.2. It also is noted that the length value will always be an integer.

It will be appreciated that a number of nucleic acids can encode a polypeptide having a particular amino acid sequence. The degeneracy of the genetic code is well known to the art; i.e., for many amino acids, there is more than one nucleotide triplet that serves as the codon for the amino acid. For example, codons in the coding sequence for a given enzyme can be modified such that optimal expression in a particular species (e.g., bacteria or fungus) is obtained, using appropriate codon bias tables for that species.

Functional fragments of any of the enzymes described herein can also be used in the methods of the document. The term “functional fragment” as used herein refers to a peptide fragment of a protein that is shorter than the full-length immature protein and has at least 25% (e.g., at least: 30%; 40%; 50%; 60%; 70%; 75%; 80%; 85%; 90%; 91%; 92%; 93%; 94%; 95%; 96%; 97%; 98%; 99%; 100%; or even greater than 100%) of the activity of the corresponding mature, full-length, wild-type protein. The functional fragment can generally, but not always, be comprised of a continuous region of the protein, wherein the region has functional activity.

This document also provides (i) functional variants of the enzymes used in the methods of the document and (ii) functional variants of the functional fragments described above. Functional variants of the enzymes and functional fragments can contain additions, deletions, or substitutions relative to the corresponding wild-type sequences. Enzymes with substitutions will generally have not more than 50 (e.g., not more than one, two, three, four, five, six, seven, eight, nine, ten, 12, 15, 20, 25, 30, 35, 40, or 50) amino acid substitutions (e.g., conservative substitutions). This applies to any of the enzymes described herein and functional fragments. A conservative substitution is a substitution of one amino acid for another with similar characteristics. Conservative substitutions include substitutions within the following groups: valine, alanine and glycine; leucine, valine, and isoleucine; aspartic acid and glutamic acid; asparagine and glutamine; serine, cysteine, and threonine; lysine and arginine; and phenylalanine and tyrosine. The nonpolar hydrophobic amino acids include alanine, leucine, isoleucine, valine, proline, phenylalanine, tryptophan and methionine. The polar neutral amino acids include glycine, serine, threonine, cysteine, tyrosine, asparagine and glutamine. The positively charged (basic) amino acids include arginine, lysine and histidine. The negatively charged (acidic) amino acids include aspartic acid and glutamic acid. Any substitution of one member of the above-mentioned polar, basic or acidic groups by another member of the same group can be deemed a conservative substitution. By contrast, a nonconservative substitution is a substitution of one amino acid for another with dissimilar characteristics.

Deletion variants can lack one, two, three, four, five, six, seven, eight, nine, ten, 11, 12, 13, 14, 15, 16, 17, 18, 19, or 20 amino acid segments (of two or more amino acids) or non-contiguous single amino acids. Additions (addition variants) include fusion proteins containing: (a) any of the enzymes described herein or a fragment thereof; and (b) internal or terminal (C or N) irrelevant or heterologous amino acid sequences. In the context of such fusion proteins, the term “heterologous amino acid sequences” refers to an amino acid sequence other than (a). A heterologous sequence can be, for example a sequence used for purification of the recombinant protein (e.g., FLAG, polyhistidine (e.g., hexahistidine), hemagglutinin (HA), glutathione-S-transferase (GST), or maltosebinding protein (MBP)). Heterologous sequences also can be proteins useful as detectable markers, for example, luciferase, green fluorescent protein (GFP), or chloramphenicol acetyl transferase (CAT). In some embodiments, the fusion protein contains a signal sequence from another protein. In certain host cells (e.g., yeast host cells), expression and/or secretion of the target protein can be increased through use of a heterologous signal sequence. In some embodiments, the fusion protein can contain a carrier (e.g., KLH) useful, e.g., in eliciting an immune response for antibody generation) or ER or Golgi apparatus retention signals. Heterologous sequences can be of varying length and in some cases can be a longer sequences than the full-length target proteins to which the heterologous sequences are attached.

Engineered hosts can naturally express none or some (e.g., one or more, two or more, three or more, four or more, five or more, or six or more) of the enzymes of the pathways described herein. Thus, a pathway within an engineered host can include all exogenous enzymes, or can include both endogenous and exogenous enzymes. Endogenous genes of the engineered hosts also can be disrupted to prevent the formation of undesirable metabolites or prevent the loss of intermediates in the pathway through other enzymes acting on such intermediates. Engineered hosts can be referred to as recombinant hosts or recombinant host cells. As described herein recombinant hosts can include nucleic acids encoding one or more of a polypeptide having fatty acid O-methyltransferase activity, a polypeptide having alcohol O-acetyltransferase activity, a polypeptide having dehydrogenase activity, a polypeptide having β-ketothiolase activity, a polypeptide having β-ketoacyl-[acp] synthase activity, a polypeptide having carboxylase activity, a polypeptide having reductase activity, a polypeptide having hydratase activity, a polypeptide having thioesterase activity, a polypeptide having monooxygenase activity, a polypeptide having demethylase activity, a polypeptide having esterase activity, or a polypeptide having transaminase activity as described herein.

In addition, the production of one or more C5 building blocks can be performed in vitro using the isolated enzymes described herein, using a lysate (e.g., a cell lysate) from a host microorganism as a source of the enzymes, or using a plurality of lysates from different host microorganisms as the source of the enzymes.

Biosynthetic Methods

The present document provides methods of producing a (C₃₋₈ hydroxyalkyl)-C(═O)OCH₃ ester. As used herein, the term (C₃₋₈ hydroxyalkyl)-C(═O)OCH₃ ester refers to a compound having the following formula:

As used herein, the term “C₃₋₈ hydroxyalkyl” refers to a saturated hydrocarbon group that may be straight-chain or branched, and is substituted by at least one hydroxyl (i.e., hydroxy or OH) group. In some embodiments, the C₃₋₈ hydroxyalkyl refers to refers to a saturated hydrocarbon group that may be straight-chain or branched, and is substituted by at least one terminal hydroxyl (OH) group. In some embodiments, the alkyl group contains 4 to 8, 4 to 7, 4 to 6, 4 to 5, 5 to 8, 5 to 7, 5 to 6, 6 to 8, 6 to 7, or 7 to 8 carbon atoms. In some embodiments, the C₃₋₈ hydroxyalkyl is a group of the following formula:

In some embodiments, the method comprises:

a) enzymatically converting a C₄₋₉ carboxylic acid to a (C₃₋₈ alkyl)-C(═O)OCH₃ ester; and

b) enzymatically converting the (C₃₋₈ alkyl)-C(═O)OCH₃ ester to (C₃₋₈ hydroxyalkyl)-C(═O)OCH₃ ester.

As used herein, the term “C₄₋₉ carboxylic acid” refers to a compound having the formula R—C(═O)OH, wherein R is a refers to a saturated hydrocarbon group (i.e., an alkyl group) that may be straight-chain or branched, wherein the compound has from 4 to 9 carbon atoms. In some embodiments, the C₄₋₉ carboxylic acid group contains 4 to 9, 4 to 8, 4 to 7, 4 to 6, 4 to 5, 5 to 9, 5 to 8, 5 to 7, 5 to 6, 6 to 9, 6 to 8, 6 to 7, 7 to 9, 7 to 8, or 8 to 9 carbon atoms. Exemplary C₄₋₉ carboxylic acids include butanoic acid (i.e., butanoate), pentanoic acid (i.e., pentanoate), hexanoic acid (i.e., hexanoate), heptanoic acid (i.e., heptanoate), octanoic acid (e.g., octanoate), nonanoic acid (i.e., nonanoate), 2-methylpentanoic acid (i.e., 2-methylpentanoate), 3-methylpentanoic acid (i.e., 3-methylpentanoate), and 4-methylpentanoic acid (i.e., 4-methylpentanoate). In some embodiments, the C₄₋₉ carboxylic acid is pentanoic acid (i.e., pentanoate).

As used herein, the term “(C₃₋₈ alkyl)-C(═O)OCH₃ ester” refers to a compound having the following formula:

As used herein, the term “C₃₋₈ alkyl” refers to a saturated hydrocarbon group that may be straight-chain or branched, having 3 to 8 carbon atoms. In some embodiments, the alkyl group contains 4 to 8, 4 to 7, 4 to 6, 4 to 5, 5 to 8, 5 to 7, 5 to 6, 6 to 8, 6 to 7, or 7 to 8, carbon atoms. Example alkyl moieties include n-butyl, isobutyl, sec-butyl, tert-butyl, n-pentyl, iso-pentyl, neo-pentyl, n-hexyl, n-heptyl, and n-octyl. In some embodiments, the C₃₋₈ alkyl is a group of the following formula:

In some embodiments, the method comprises:

a) enzymatically converting a C₄₋₉ carboxylic acid to a (C₃₋₈ alkyl)-C(═O)OCH₃ ester; and

b) enzymatically converting the (C₃₋₈ alkyl)-C(═O)OCH₃ ester to (C₃₋₈ hydroxyalkyl)-C(═O)OCH₃ ester.

In some embodiments, the C₄₋₉ carboxylic acid is enzymatically converted to the (C₃₋₈ alkyl)-C(═O)OCH₃ ester using a polypeptide having fatty acid O-methyltransferase activity. In some embodiments, the polypeptide having fatty acid O-methyltransferase activity has at least 70% sequence identity to an amino acid sequence set forth in SEQ ID NO:23, SEQ ID NO:24, or SEQ ID NO:25.

In some embodiments, the (C₃₋₈ alkyl)-C(═O)OCH₃ ester is enzymatically converted to the (C₃₋₈ hydroxyalkyl)-C(═O)OCH₃ ester using a polypeptide having monooxygenase activity. In some embodiments, the monooxygenase is classified under EC 1.14.14.- or EC 1.14.15.-. In some embodiments, the monooxygenase has at least 70% sequence identity to an amino acid sequence set forth in SEQ ID NO:28 or SEQ ID NO:29.

In some embodiments, the C₄₋₉ carboxylic acid is enzymatically produced from C₄₋₉ alkanoyl-CoA. As used herein, the term “C₄₋₉ alkanoyl-CoA” refers to a compound having the following formula:

wherein the C₃₋₈ alkyl group is as defined herein. In some embodiments, the C₃₋₈ alkyl is a group of the following formula:

In some embodiments, a polypeptide having thioesterase activity enzymatically produces the C₄₋₉ carboxylic acid from C₄₋₉ alkanoyl-CoA. In some embodiments, the thioesterase has at least 70% sequence identity to the amino acid sequence set forth in SEQ ID NO: 1. In some embodiments, a polypeptide having butanal dehydrogenase activity and a polypeptide having aldehyde dehydrogenase activity enzymatically produces the C₄₋₉ carboxylic acid from the C₄₋₉ alkanoyl-CoA.

In some embodiments, the method of producing a (C₃₋₈ hydroxyalkyl)-C(═O)OCH₃ ester is a method of producing 5-hydroxypentanoate methyl ester, said method comprising:

a) enzymatically converting pentanoate to pentanoate methyl ester; and

b) enzymatically converting the pentanoate methyl ester to 5-hydroxypentanoate methyl ester.

In some embodiments, pentanoate is enzymatically converted to pentanoate 5 methyl ester using a polypeptide having fatty acid O-methyltransferase activity. In some embodiments, the polypeptide having fatty acid O-methyltransferase activity has at least 70% sequence identity to an amino acid sequence set forth in SEQ ID NO:23, SEQ ID NO:24, or SEQ ID NO:25. In some embodiments, the polypeptide having fatty acid O-methyltransferase activity is classified under EC 12.1.1.15.

In some embodiments, pentanoate methyl ester is enzymatically converted to 5-hydroxypentanoate methyl ester using a polypeptide having monooxygenase activity. In some embodiments, the polypeptide having monooxygenase activity has at least 70% sequence identity to an amino acid sequence set forth in SEQ ID NO:28 or SEQ ID NO:29. In some embodiments, the polypeptide having monooxygenase activity is classified under EC 1.14.14.- or EC 1.14.15.-.

In some embodiments, pentanoate is enzymatically produced from pentanoyl-CoA. In some embodiments, a polypeptide having thioesterase activity enzymatically produces pentanoate from pentanoyl-CoA. In some embodiments, the polypeptide having thioesterase activity has at least 70% sequence identity to the amino acid sequence set forth in SEQ ID NO:1. In some embodiments, a polypeptide having butanal dehydrogenase activity and a polypeptide having aldehyde dehydrogenase activity enzymatically produce pentanoate from pentanoyl-CoA.

The present document further provides methods of producing one or more terminal hydroxy-substituted (C₄₋₉ alkyl)-OC(═O)—(C₃₋₈ alkyl) esters. As used herein, the term (C₄₋₉ alkyl)-OC(═O)—(C₃₋₈ alkyl) ester” refers to a compound having the following formula:

wherein the C₃₋₈ alkyl group is as defined herein. As used herein the term “terminal hydroxy-substituted “(C₄₋₉ alkyl)-OC(═O)—(C₃₋₈ alkyl) ester” refers to a compound having the following formula:

wherein at least one of the alkyl groups (i.e., at least one of the C₄₋₉ alkyl and C₃₋₈ alkyl groups) is subsequently substituted by at least one terminal hydroxy (—OH) group, and the C₃₋₈ alkyl is as defined herein. As used herein, the term “C₄₋₉ alkyl” refers to a saturated hydrocarbon group that may be straight-chain or branched, having 4 to 9 carbon atoms. In some embodiments, the alkyl group contains 4 to 9, 4 to 8, 4 to 7, 4 to 6, 4 to 5, 5 to 9, 5 to 8, 5 to 7, 5 to 6, 6 to 9, 6 to 8, 6 to 7, 7 to 9, 7 to 8, or 8 to 9 carbon atoms. Example alkyl moieties include n-butyl, isobutyl, sec-butyl, tert-butyl, n-pentyl, iso-pentyl, neo-pentyl, n-hexyl, n-heptyl, n-octyl, and n-nonyl. In some embodiments, one of the alkyl groups is substituted by at least one terminal hydroxy group. In some embodiments, each of the alkyl groups is substituted by at least one terminal hydroxy group. In some embodiments, one of the alkyl groups is substituted by one terminal hydroxy group. In some embodiments, each of the alkyl groups is substituted by one terminal hydroxy group. In some embodiments, the terminal hydroxy-substituted (C₄₋₉ alkyl)-OC(═O)—(C₃₋₈ alkyl) ester is selected from the group consisting of:

In some embodiments, the method includes:

a) enzymatically converting C₄₋₉ alkanoyl-CoA to a (C₄₋₉ alkyl)-OC(═O)—(C₃₋₈ alkyl) ester; and

b) enzymatically converting the (C₄₋₉ alkyl)-OC(═O)—(C₃₋₈ alkyl) ester to any of (C₄₋₉ alkyl)-OC(═O)—(C₃₋₈ hydroxyalkyl) ester, (C₄₋₉ hydroxyalkyl)-OC(═O)—(C₃₋₈ hydroxyalkyl) ester, or (C₄₋₉ hydroxyalkyl)-OC(═O)—(C₃₋₈ alkyl) ester.

In some embodiments, C₄₋₉ alkanoyl-CoA is enzymatically converted to the (C₄₋₉ alkyl)-OC(═O)—(C₃₋₈ alkyl) ester using a polypeptide having alcohol O-acetyltransferase activity. In some embodiments, the alcohol O-acetyltransferase has at least 70% sequence identity to the amino acid sequence set forth in SEQ ID NO: 26.

In some embodiments, the (C₄₋₉ alkyl)-OC(═O)—(C₃₋₈ alkyl) ester is enzymatically converted to any of (C₄₋₉ alkyl)-OC(═O)—(C₃₋₈ hydroxyalkyl) ester, (C₄₋₉ hydroxyalkyl)-OC(═O)—(C₃₋₈ hydroxyalkyl) ester, or (C₄₋₉ hydroxyalkyl)-OC(═O)—(C₃₋₈ alkyl) ester using a polypeptide having monooxygenase activity. In some embodiments, the polypeptide having monooxygenase activity is classified under EC 1.14.14.- or EC 1.14.15.-.

In some embodiments, the method further includes enzymatically converting (C₄₋₉ hydroxyalkyl)-OC(═O)—(C₃₋₈ hydroxyalkyl) ester or (C₄₋₉ hydroxyalkyl)-OC(═O)—(C₃₋₈ alkyl) ester to a C₄₋₉ hydroxyalkanoate. In some embodiments, a polypeptide having esterase activity enzymatically converts (C₄₋₉ hydroxyalkyl)-OC(═O)—(C₃₋₈ hydroxyalkyl) ester or (C₄₋₉ hydroxyalkyl)-OC(═O)—(C₃₋₈ alkyl) ester to the C₄₋₉ hydroxyalkanoate.

As used herein, the term C₄₋₉ hydroxyalkanoate refers to a compound having the following formula:

wherein the C₃₋₈ hydroxyalkyl is as defined herein. Example C₄₋₉ hydroxyalkanoates include, but are not limited to, 5-hydroxypentanoate (i.e., 5-hydroxypentanoic acid), 4-hydroxypentanoate (i.e., 4-hydroxypentanoic acid), 3-hydroxypentanoate (i.e., 3-hydroxypentanoic acid), and the like. It is understood by those skilled in the art that the specific form will depend on pH (e.g., neutral or ionized forms, including any salt forms thereof). In some embodiments, the C₃₋₈ hydroxyalkyl is a group having the following formula:

In some embodiments, the method of producing one or more hydroxy-substituted (C₃₋₈ alkyl)-OC(═O)—(C₃₋₈ alkyl) esters is a method of producing one or more pentanoic acid pentyl hydroxyl esters. In some embodiments, the method includes:

a) enzymatically converting pentanoyl-CoA to pentanoic acid pentyl ester; and

b) enzymatically converting pentanoic acid pentyl ester to any of 5-hydroxypentanoic acid pentyl ester, 5-hydroxypentanoic acid 5-hydroxypentyl ester, or pentanoic acid 5-hydroxypentyl ester.

In some embodiments, pentanoyl-CoA is enzymatically converted to pentanoic acid pentyl ester using a polypeptide having alcohol O-acetyltransferase activity. In some embodiments, the polypeptide having alcohol O-acetyltransferase activity has at least 70% sequence identity to the amino acid sequence set forth in SEQ ID NO: 26.

In some embodiments, pentanoic acid pentyl ester is enzymatically converted to any of 5-hydroxypentanoic acid pentyl ester, 5-hydroxypentanoic acid 5-hydroxypentyl ester and/or pentanoic acid 5-hydroxypentyl ester using a polypeptide having monooxygenase activity. In some embodiments, the polypeptide having monooxygenase activity is classified under EC 1.14.14.- or EC 1.14.15.-.

In some embodiments, the method further includes enzymatically converting 5-hydroxypentanoic acid 5-hydroxypentyl ester or 5-hydroxypentanoic acid pentyl ester to 5-hydroxypentanoate. In some embodiments, a polypeptide having esterase activity enzymatically converts 5-hydroxypentanoic acid 5-hydroxypentyl ester or 5-hydroxypentanoic acid pentyl ester to 5-hydroxypentanoate.

In some embodiments, the method can include enzymatically converting 5-hydroxypentanoic acid 5-hydroxypentyl ester or pentanoic acid 5-hydroxypentyl ester to 1,5-pentanediol. In some embodiments, a polypeptide having esterase activity enzymatically converts 5-hydroxypentanoic acid 5-hydroxypentyl ester or pentanoic acid 5-hydroxypentyl ester to 1,5-pentanediol.

In some embodiments, the method further includes enzymatically converting 5-hydroxypentanoic acid pentyl ester, 5-hydroxypentanoic acid 5-hydroxypentyl ester, or pentanoic acid 5-hydroxypentyl ester to 5-hydroxypentanoate and/or 1,5-pentanediol. In some embodiments, a polypeptide having esterase activity enzymatically converts 5-hydroxypentanoic acid pentyl ester, 5-hydroxypentanoic acid 5-hydroxypentyl ester, or pentanoic acid 5-hydroxypentyl ester to 5-hydroxypentanoate and/or 1,5-pentanediol.

In some embodiments, the method further includes enzymatically converting 1,5-pentanediol to 5-hydroxypentanal. In some embodiments, a polypeptide having alcohol dehydrogenase activity enzymatically converts 1,5-pentanediol to 5-hydroxypentanal.

In some embodiments, the method further includes enzymatically converting 5-hydroxypentanal to 5-hydroxypentanoate. In some embodiments, a polypeptide having aldehyde dehydrogenase activity enzymatically converts 5-hydroxypentanal to 5-hydroxypentanoate.

In some embodiments, the method further includes enzymatically converting 5-hydroxypentanoate methyl ester to 5-hydroxypentanoate. In some embodiments, a polypeptide having demethylase or esterase activity enzymatically converts 5-hydroxypentanoate methyl ester to 5-hydroxypentanoate.

In some embodiments, the method further includes enzymatically converting 5-hydroxypentanoate to a product selected from the group consisting of glutaric acid, glutarate semialdehyde, 5-aminopentanoate, cadaverine, and 1,5-pentanediol.

In some embodiments, the method includes enzymatically converting 5-hydroxypentanoate to glutarate semialdehyde using a polypeptide having alcohol dehydrogenase activity, a polypeptide having 6-hydroxyhexanoate dehydrogenase activity, a polypeptide having 5-hydroxypentanoate dehydrogenase activity, a polypeptide having 4-hydroxybutyrate dehydrogenase activity, or a polypeptide having monooxygenase activity.

In some embodiments, the method further includes enzymatically converting glutarate semialdehyde to glutaric acid using a polypeptide having 7-oxoheptanoate dehydrogenase activity, a polypeptide having 6-oxohexanoate dehydrogenase activity, a polypeptide having 5-oxopentanoate dehydrogenase activity, a polypeptide having aldehyde dehydrogenase activity, or a polypeptide having monooxygenase activity.

In some embodiments, the method further includes enzymatically converting glutarate semialdehyde to 5-aminopentanoate. In some embodiments, a ω-transaminase enzymatically converts glutarate semialdehyde to 5-aminopentanoate.

In some embodiments, the method further includes enzymatically converting 5-aminopentanoate to cadaverine. In some embodiments, the method further includes enzymatically converting glutarate semialdehyde to cadaverine. In some embodiments, glutarate semialdehyde or 5-aminopentanoate is enzymatically converted to cadaverine using a polypeptide having carboxylate reductase activity and a polypeptide having ω-transaminase activity and optionally one or more of a polypeptide having N-acetyl transferase activity, a polypeptide having acetylputrescine deacetylase activity, and a polypeptide having alcohol dehydrogenase activity.

In some embodiments, 5-hydroxypentanoate is enzymatically converted to 1,5-pentanediol using a polypeptide having carboxylate reductase activity and a polypeptide having alcohol dehydrogenase activity.

In some embodiments, said method further comprises enzymatically converting 1,5-pentanediol to cadaverine. In some embodiments, a polypeptide having alcohol dehydrogenase activity and a polypeptide having ω-transaminase activity enzymatically converts 1,5-pentanediol cadaverine.

In some embodiments, a polypeptide having carboxylate reductase activity, a polypeptide having ω-transaminase activity, and a polypeptide having alcohol dehydrogenase activity enzymatically converts 5-hydroxypentanoate to cadaverine. In some embodiments, the ω-transaminase has at least 70% sequence identity to any one of the amino acid sequences set forth in SEQ ID NO. 8-13.

In some embodiments, pentanoyl-CoA is produced from acetyl-CoA and propanoyl-CoA via two cycles of CoA-dependent carbon chain elongation. In some embodiments, each of said two cycles of CoA-dependent carbon chain elongation comprises using a polypeptide having β-ketothiolase activity or a polypeptide having acetyl-CoA carboxylase activity and a polypeptide having β-ketoacyl-[acp] synthase activity, a polypeptide having 3-hydroxyacyl-CoA dehydrogenase activity or a polypeptide having 3-oxoacyl-CoA reductase activity, a polypeptide having enoyl-CoA hydratase activity, and a polypeptide having trans-2-enoyl-CoA reductase activity to form pentanoyl-CoA from acetyl-CoA and propanoyl-CoA.

Enzymes Converting Pentanoate or Pentanoyl-CoA to 5-Hydroxypentanoate

As depicted in FIG. 7, pentanoate methyl ester can be formed from pentanoate using a polypeptide having fatty acid O-methyltransferase activity, such as the fatty acid O-methyltransferase classified, for example, under EC 2.1.1.15. For example, the polypeptide having fatty acid O-methyltransferase activity can be obtained from Mycobacterium marinum (GenBank Accession No. ACC41782.1. SEQ ID NO:23); Mycobacterium smegmatis (see GenBank Accession No. ABK73223.1, SEQ ID NO: 24), or Pseudomonas putida (see GenBank Accession No. CAA39234.1, SEQ ID NO: 25).

Pentanoate methyl ester can be converted to 5-hydroxypentanoate methyl ester using a polypeptide having monooxygenase activity classified, for example, under EC 1.14.14.- or EC 1.14.15.- (e.g., EC 1.14.15.1 or EC 1.14.15.3) For example, a polypeptide having monooxygenase activity can be, for example, from the CYP153A family (SEQ ID NOs:14-16), the CYP52A3 family (See Genbank Accession No: BAA00371.1, SEQ ID NO: 29) or the alkB family such as the gene product of alkBGT from Pseudomonas putida (See Genbank Accession No. CAB51047.1, SEQ ID NO: 28). See, FIG. 7.

5-hydroxypentanoate methyl ester can be converted to 5-hydroxypentanoate using a polypeptide having demethylase activity classified, for example, under EC 2.1.1.- such as the gene product of ligM (see GenBank Accession No. BAD61059.1; SEQ ID NO:31) or desA (GenBank Accession No. BAC59257.1; SEQ ID NO:32) or using a polypeptide having esterase activity classified, for example under EC 3.1.1.- such as the gene product of EstC (see GenBank Accession No. AAC60471.2, SEQ ID NO: 27).

As depicted in FIG. 7, pentanoyl-CoA can be converted to pentanoic acid pentyl ester using a polypeptide having alcohol O-acetyltransferase activity classified, for example, under EC 2.3.1.-(e.g., EC 2.3.1.84) such as the gene product of Eht1 (Genbank Accession No: CAA85138.1, SEQ ID NO: 26).

Pentanoic acid pentyl ester can be converted to 5-hydroxypentanoic acid pentyl ester and/or 5-hydroxypentanoic acid 5-hydroxypentyl ester using a polypeptide having monooxygenase activity classified, for example, under EC 1.14.14.- or EC 1.14.15.- (e.g., EC 1.14.15.1 or EC 1.14.15.3) For example, a polypeptide having monooxygenase activity can be, for example, from the CYP153A family, the CYP52A3 family (Genbank Accession No: BAA00371.1, SEQ ID NO: 29) or the alkB family such as the gene product of alkBGT from Pseudomonas putida (Genbank Accession No. CAB51047.1, SEQ ID NO: 28). See, FIG. 7.

5-hydroxypentanoic acid pentyl ester and 5-hydroxypentanoic acid 5-hydroxypentyl can be converted to 5-hydroxypentanoate using a polypeptide having esterase activity classified, for example, under EC 3.1.1.- (EC 3.1.1.1 or EC 3.1.1.6) such as the gene product of EstC (see GenBank Accession No. AAC60471.2, SEQ ID NO: 27).

For example, the monooxygenase CYP153A family classified, for example, under EC 1.14.15.- (e.g., EC 1.14.15.1 or EC 1.14.15.3) is soluble and has regio-specificity for terminal hydroxylation, accepting medium chain length substrates (see, e.g., Koch et al., Appl. Environ. Microbiol., 2009, 75(2), 337-344; Funhoff et al., 2006, J. Bacteriol., 188(44): 5220-5227; Van Beilen & Funhoff, Current Opinion in Biotechnology, 2005, 16, 308-314; Nieder and Shapiro, J. Bacteriol., 1975, 122(1), 93-98). Although non-terminal hydroxylation is observed in vitro for CYP153A, in vivo only 1-hydroxylation occurs (see, Funhoff et al., 2006, supra).

The substrate specificity and activity of terminal monooxygenases has been broadened via successfully, reducing the chain length specificity of CYP153A to below C8 (Koch et al., 2009, supra).

In some embodiments, pentanoate can be enzymatically formed from pentanoyl-CoA using a polypeptide having thioesterase activity classified under EC 3.1.2.-, such as the gene product of YciA, tesB (GenBank Accession No. AAA24665.1, SEQ ID NO: 1) or Acot13 (Cantu et al., Protein Science, 2010, 19, 1281-1295; Zhuang et al., Biochemistry, 2008, 47(9):2789-2796; Naggert et al., J. Biol. Chem., 1991, 266(17): 11044-11050), the acyl-[acp] thioesterase from a Lactobacillus brevis (GenBank Accession No. ABJ63754.1, SEQ ID NO:33), or a Lactobacillus plantarum (GenBank Accession No. CCC58182.1, SEQ ID NO:34). Such acyl-[acp] thioesterases have C6-C8 chain length specificity (see, for example, Jing et al., 2011, BMC Biochemistry, 12(44)). See, FIG. 3.

In some embodiments, pentanoate can be enzymatically formed from pentanoyl-CoA using a polypeptide having butanal dehydrogenase activity classified, for example, under EC 1.2.1.- such as EC 1.2.1.10 or EC 1.2.1.57 (see, e.g., GenBank Accession No. AAD39015, SEQ ID NO:30) (e.g., the gene product of PduB or PduD) or an aldehyde dehydrogenase classified, for example, under EC 1.2.1.- such as EC 1.2.1.3 or EC 1.2.1.4 (see, Ho & Weiner, J. Bacteriol., 2005, 187(3):1067-1073). See, FIG. 3.

Enzymes Generating Pentanoyl-CoA for Conversion to a C5 Building Block

As depicted in FIG. 1 and FIG. 2, pentanoyl-CoA can be formed from acetyl-CoA or propanoyl-CoA via two cycles of CoA-dependent carbon chain elongation using either NADH or NADPH dependent enzymes.

In some embodiments, a CoA-dependent carbon chain elongation cycle comprises using a polypeptide having β-ketothiolase activity or a polypeptide having acetyl-CoA carboxylase activity and a polypeptide having β-ketoacyl-[acp] synthase activity, a polypeptide having 3-hydroxyacyl-CoA dehydrogenase activity or a polypeptide having 3-oxoacyl-CoA reductase activity, a polypeptide having enoyl-CoA hydratase activity and a polypeptide having trans-2-enoyl-CoA reductase activity. A polypeptide having fi-ketothiolase activity can convert propanoyl-CoA to 3-oxopentanoyl-CoA and can convert pentanoyl-CoA to 3-oxopentanoyl-CoA. A polypeptide having acetyl-CoA carboxylase activity can convert acetyl-CoA to malonyl-CoA. A polypeptide having acetoacetyl-CoA synthase activity can convert malonyl-CoA to acetoacetyl-CoA. A polypeptide having 3-hydroxybutyryl-CoA dehydrogenase activity can convert 3-oxopentanoyl-CoA to 3-hydroxypentanoyl CoA. A polypeptide having 3-oxoacyl-CoA reductase/3-hydroxyacyl-CoA dehydrogenase activity can convert 3-oxopentanoyl-CoA to 3-hydroxypentanoyl-CoA. A polypeptide having enoyl-CoA hydratase activity can convert 3-hydroxypentanoyl-CoA to pent-2-enoyl-CoA and can convert 3-hydroxypentanoyl-CoA to pent-2-enoyl-CoA. A polypeptide having trans-2-enoyl-CoA reductase activity can convert pent-2-enoyl-CoA to pentanoyl-CoA and can convert pent-2-enoyl-CoA to pentanoyl-CoA. See FIGS. 1 and 2.

In some embodiments, a polypeptide having β-ketothiolase activity can be classified under EC 2.3.1.16, such as the gene product of bktB (See, e.g., Genbank Accession AAC38322.1). The polypeptide having β-ketothiolase activity encoded by bktB from Cupriavidus necator accepts propanoyl-CoA and pentanoyl-CoA as substrates. When pentanoyl-CoA is the substrate, the CoA-activated C5 aliphatic backbone (3-oxopentanoyl-CoA) is produced (see, e.g., Haywood et al., FEMS Microbiology Letters, 1988, 52:91-96; Slater et al., J. Bacteriol., 1998, 180(8):1979-1987). The polypeptide having β-ketothiolase activity encoded by paaJ (See, e.g., Genbank Accession No. AAC54479.1), catF and pcaF can be classified under, for example, EC 2.3.1.174. The polypeptide having β-ketothiolase activity encoded by paaJ condenses acetyl-CoA and succinyl-CoA to 3-oxoadipyl-CoA (see, for example, Fuchs et al., 2011, Nature Reviews Microbiology, 9, 803-816; Gobel et al., 2002, J. Bacteriol., 184(1), 216-223) See FIGS. 1 and 2.

In some embodiments, a polypeptide having acetyl-CoA carboxylase activity can be classified, for example, under EC 6.4.1.2. In some embodiments, a polypeptide having β-ketoacyl-[acp] synthase activity can be classified, for example, under 2.3.1.180 such as the gene product of FabH from Staphylococcus aereus (Qiu et al., 2005, Protein Science, 14: 2087-2094). See FIGS. 1 and 2.

In some embodiments, a polypeptide having 3-hydroxyacyl-CoA dehydrogenase activity or a polypeptide having 3-oxoacyl-CoA dehydrogenase activity can be classified under EC 1.1.1.-. For example, the polypeptide having 3-hydroxyacyl-CoA dehydrogenase activity can be classified under EC 1.1.1.35, such as the gene product of fadB (FIG. 1); classified under EC 1.1.1.157, such as the gene product of hbd (can be referred to as a 3-hydroxybutyryl-CoA dehydrogenase) (FIG. 1); or classified under EC 1.1.1.36, such as the acetoacetyl-CoA reductase gene product of phaB (Liu & Chen, Appl. Microbiol. Biotechnol., 2007, 76(5):1153-1159; Shen et al., Appl. Environ. Microbiol., 2011, 77(9):2905-2915; Budde et al., J. Bacteriol., 2010, 192(20):5319-5328) (FIG. 2).

In some embodiments, a polypeptide having 3-oxoacyl-CoA reductase activity can be classified under EC 1.1.1.100, such as the gene product of fabG (Budde et al., J. Bacteriol., 2010, 192(20):5319-5328; Nomura et al., Appl. Environ. Microbiol., 2005, 71(8):4297-4306). FIG. 2.

In some embodiments, a polypeptide having enoyl-CoA hydratase activity can be classified under EC 4.2.1.17, such as the gene product of crt (Genbank Accession No. AAA95967.1) (FIG. 1), or classified under EC 4.2.1.119, such as the gene product of phaJ (Genbank Accession No. BAA21816.1) (FIG. 2) (Shen et al., 2011, supra; Fukui et al., J. Bacteriol., 1998, 180(3):667-673).

In some embodiments, a polypeptide having trans-2-enoyl-CoA reductase activity can be classified under EC 1.3.1.38 (FIG. 2), EC 1.3.1.8 (FIG. 2), or EC 1.3.1.44 (FIG. 1), such as the gene product of ter (Genbank Accession No. AAW66853.1) (Nishimaki et al., J. Biochem., 1984, 95:1315-1321; Shen et al., 2011, supra) or tdter (Genbank Accession No. AAS11092.1) (Bond-Watts et al., Biochemistry, 2012, 51:6827-6837).

Enzymes Generating the Terminal Carboxyl Groups in the Biosynthesis of a C5 Building Block

As depicted in FIGS. 4, 5, and 7, a terminal carboxyl group can be enzymatically formed using a polypeptide having thioesterase activity, a polypeptide having aldehyde dehydrogenase activity, a polypeptide having 7-oxoheptanoate dehydrogenase activity, a polypeptide having 6-oxohexanoate dehydrogenase activity, a polypeptide having 5-oxopentanoate dehydrogenase activity, a polypeptide having monooxygenase activity, a polypeptide having esterase activity, or a polypeptide having demethylase activity.

In some embodiments, the first terminal carboxyl group is enzymatically formed by a polypeptide having syringate O-demethylase activity classified under EC 2.1.1.-such as the gene products of ligM (see GenBank Accession No. BAD61059.1; SEQ ID NO:31) or desA (GenBank Accession No. BAC59257.1; SEQ ID NO:32) or an esterase classified under EC 3.1.1.- such as the gene product of EstC (see, e.g., GenBank Accession No. AAC60471.2, SEQ ID NO: 27) See, e.g., FIG. 7.

In some embodiments, the first terminal carboxyl group is enzymatically formed by a polypeptide having aldehyde dehydrogenase activity classified, for example, under EC 1.2.1.3 or EC 1.2.1.4.

In some embodiments, the second terminal carboxyl group leading to the synthesis of glutaric acid is enzymatically formed by a polypeptide having aldehyde dehydrogenase activity classified, for example, under EC 1.2.1.3 (see, Guerrillot & Vandecasteele, Eur. J. Biochem., 1977, 81, 185-192). See FIG. 4.

In some embodiments, the second terminal carboxyl group leading to the synthesis of glutaric acid is enzymatically formed by a polypeptide having dehydrogenase activity classified under EC 1.2.1.- such as a 5-oxopentanoate dehydrogenase (e.g., the gene product of CpnE), a 6-oxohexanoate dehydrogenase (e.g., the gene product of ChnE from Acinetobacter sp.), a 7-oxoheptanoate dehydrogenase (e.g., the gene product of ThnG from Sphingomonas macrogolitabida) (Iwaki et al., Appl. Environ. Microbiol., 1999, 65(11), 5158-5162; López-Sánchez et al., Appl. Environ. Microbiol., 2010, 76(1), 110-118). For example, a polypeptide having 5-oxopentanoate dehydrogenase activity can be classified under EC 1.2.1.20. For example, a polypeptide having 6-oxohexanoate dehydrogenase activity can be classified under EC 1.2.1.63. For example, a polypeptide having 7-oxoheptanoate dehydrogenase activity can be classified under EC 1.2.1.-. See, FIG. 4.

In some embodiments, the second terminal carboxyl group leading to the synthesis of glutaric acid is enzymatically formed by a polypeptide having monooxygenase activity in the cytochrome P450 family such as CYP4F3B (see, e.g., Sanders et al., J. Lipid Research, 2005, 46(5):1001-1008; Sanders et al., The FASEB Journal, 2008, 22(6):2064-2071). See, FIG. 4.

The utility of ω-oxidation in introducing carboxyl groups into alkanes has been demonstrated in the yeast Candida tropicalis, leading to the synthesis of adipic acid (Okuhara et al., Agr. Biol. Chem., 1971, 35(9), 1376-1380).

Enzymes Generating the Terminal Amine Groups in the Biosynthesis of a C5 Building Block

As depicted in FIG. 5 and FIG. 6, terminal amine groups can be enzymatically formed using a polypeptide having ω-transaminase activity or a polypeptide having deacetylase activity.

In some embodiments, the first terminal amine group leading to the synthesis of 5-aminopentanoic acid, 5-aminopentanal, or 5-aminopentanol is enzymatically formed by a ω-transaminase classified, for example, under EC 2.6.1.- such as EC 2.6.1.18, EC 2.6.1.19, EC 2.6.1.29, EC 2.6.1.48, or EC 2.6.1.82 such as that obtained from Chromobacterium violaceum (Genbank Accession No. AAQ59697.1, SEQ ID NO: 8), Pseudomonas aeruginosa (Genbank Accession No. AAG08191.1, SEQ ID NO: 9), Pseudomonas syringae (Genbank Accession No. AAY39893.1, SEQ ID NO: 10), Rhodobacter sphaeroides (Genbank Accession No. ABA81135.1, SEQ ID NO: 11), Vibrio fluvialis (Genbank Accession No. AAA57874.1, SEQ ID NO: 13), Streptomyces griseus, or Clostridium viride. An additional polypeptide having ω-transaminase activity that can be used in the methods and hosts described herein is from Escherichia coli (Genbank Accession No. AAA57874.1, SEQ ID NO: 12). Some of the polypeptides having ω-transaminases activity classified, for example, under EC 2.6.1.29 or EC 2.6.1.82 are polypeptides having diamine ω-transaminases activity (e.g., SEQ ID NO:12). See, e.g., FIGS. 5 and 6.

The reversible polypeptide having ω-transaminase activity from Chromobacterium violaceum (Genbank Accession No. AAQ59697.1, SEQ ID NO: 8) has demonstrated analogous activity accepting 6-aminohexanoic acid as amino donor, thus forming the first terminal amine group in adipate semialdehyde (Kaulmann et al., Enzyme and Microbial Technology, 2007, 41, 628-637).

The reversible polypeptide having 4-aminobutyrate:2-oxoglutarate transaminase activity from Streptomyces griseus has demonstrated analogous activity for the conversion of 6-aminohexanoate to adipate semialdehyde (Yonaha et al., Eur. J. Biochem., 1985, 146, 101-106).

The reversible polypeptide having 5-aminovalerate transaminase activity from Clostridium viride has demonstrated analogous activity for the conversion of 6-aminohexanoate to adipate semialdehyde (Barker et al., J. Biol. Chem., 1987, 262(19), 8994-9003).

In some embodiments, the second terminal amine group leading to the synthesis of cadaverine is enzymatically formed by a polypeptide having diamine transaminase activity. For example, the second terminal amino group can be enzymatically formed by a polypeptide having diamine transaminase activity classified, for example, under EC 2.6.1.-, e.g., EC 2.6.1.29 or classified, for example, under EC 2.6.1.82, such as the gene product of YgjG from E. coli (Genbank Accession No. AAA57874.1, SEQ ID NO: 12). See, FIG. 6.

The gene product of ygjG accepts a broad range of diamine carbon chain length substrates, such as putrescine, cadaverine and spermidine (Samsonova et al., BMC Microbiology, 2003, 3:2).

The polypeptide having diamine transaminase activity from E. coli strain B has demonstrated activity for 1,7 diaminopentane (Kim, The Journal of Chemistry, 1964, 239(3), 783-786).

In some embodiments, the second terminal amine group leading to the synthesis of cadaverine is enzymatically formed by a polypeptide having deacetylase activity classified, for example, under EC 3.5.1.62 such as a polypeptide having acetylputrescine deacetylase activity. The polypeptide having acetylputrescine deacetylase activity from Micrococcus luteus K-11 accepts a broad range of carbon chain length substrates, such as acetylputrescine, acetylcadaverine and N⁸-acetylspermidine (see, for example, Suzuki et al., 1986, BBA—General Subjects, 882(1):140-142).

Enzymes Generating the Terminal Hydroxyl Groups in the Biosynthesis of a C5 Building Block

As depicted in FIG. 8, a terminal hydroxyl group can be enzymatically forming using a polypeptide having alcohol dehydrogenase activity. For example, the second terminal hydroxyl group leading to the synthesis of 1,7 pentanediol is enzymatically formed by a polypeptide having alcohol dehydrogenase activity classified under EC 1.1.1.- (e.g., EC 1.1.1.1, 1.1.1.2, 1.1.1.21, or 1.1.1.184).

A first terminal hydroxyl group can be enzymatically formed with a polypeptide having monoxygenase activity as discussed above with respect to the formation of 5-hydroxypentanoate methyl ester in FIG. 7.

As depicted in FIG. 8, pentanoyl-CoA can be converted to pentanoic acid pentyl ester using a polypeptide having alcohol O-acetyltransferase activity classified, for example, under EC 2.3.1.-(84) such as the gene product of Eht1 (Genbank Accession No: CAA85138.1, SEQ ID NO: 26).

Pentanoic acid pentyl ester can be converted to 5-hydroxypentanoic acid 5-hydroxypentyl ester using a polypeptide having monooxygenase activity classified, for example, under EC 1.14.14.- or EC 1.14.15.- (EC 1.14.15.1 or EC 1.14.15.3). Pentanoic acid pentyl ester can be converted to pentanoic acid 5-hydroxypentyl ester using a polypeptide having monooxygenase activity classified, for example, under EC 1.14.14.- or EC 1.14.15.- (1,3). For example, a polypeptide having monooxygenase activity can be, for example, from the CYP153A family, the CYP52A3 family or the alkB family such as the gene product of alkBGT from Pseudomonas putida. See, FIG. 7.

Pentanoic acid 5-hydroxypentyl ester and 5-hydroxypentanoic acid 5-hydroxypentyl can be converted to 1,5-pentanediol using a polypeptide having esterase activity classified, for example, under EC 3.1.1.- (e.g., EC 3.1.1.1 or EC 3.1.1.6) such as the gene product of EstC (see GenBank Accession No. AAC60471.2, SEQ ID NO: 27).

Biochemical Pathways Pathways to Propanoyl-CoA

In some embodiments, propanoyl-Coenzyme A (CoA) is a precursor leading to one or more central precursors in the synthesis of one or more C5 building blocks (see, e.g., FIG. 9).

In some embodiments, propanoyl-CoA is synthesized from the central metabolite succinyl-CoA by conversion of succinyl-CoA to (2R)-methylmalonyl-CoA by a polypeptide having methylmalonyl-CoA mutase activity classified, for example, under EC 5.4.99.2; followed by conversion to (2S)-methylmalonyl-CoA by a polypeptide having methylmalonyl-CoA epimerase activity classified, for example, under EC 5.1.99.1; followed by conversion to propanoyl-CoA by a polypeptide having methylmalonyl-CoA carboxytransferase activity classified, for example, under EC 2.1.3.1 or a polypeptide having methylmalonyl-CoA decarboxylase activity classified, for example, under EC 4.1.1.41. See e.g., FIG. 9.

In some embodiments, propanoyl-CoA is synthesized from the central metabolite, L-threonine, by conversion of L-threonine to 2-oxobutyrate by a polypeptide having threonine ammonia lyase activity classified, for example, under EC 4.3.1.19; followed by conversion to propanoyl-CoA by a polypeptide having 2-ketobutyrate formate-lyase activity classified, for example, under EC 2.3.1.- such as the gene product of tdcE (Tseng et al., Microbial Cell Factories, 2010, 9:96). See, e.g., FIG. 9.

In some embodiments, propanoyl-CoA is synthesized from 1,2-propanediol by conversion to propanal by a polypeptide having propanediol dehydratase activity classified, for example, under EC 4.2.1.28; followed by conversion to propanoyl-CoA by a polypeptide having CoA-dependent propionaldehyde dehydrogenase activity such as the gene product of pduP (Luo et al., Bioresource Technology, 2012, 103:1-6). See, e.g., FIG. 9.

In some embodiments, propanoyl-CoA is synthesized from the carbon source, levulinic acid, by conversion of levulinic acid to levulinyl-CoA by a polypeptide having acyl-CoA synthetase or ligase activity classified, for example, under EC 6.2.1.-; followed by conversion to propanoyl-CoA by a transferase classified, for example, under EC 2.3.1.- (Jaremko and Yu, J. Biotechnol., 2011, 155:293-298). See, e.g., FIG. 9.

In some embodiments, propanoyl-CoA is synthesized from the central metabolite, pyruvate, by conversion of pyruvate to L-lactate by a polypeptide having L-lactate dehydrogenase activity classified, for example, under EC 1.1.1.27; followed by conversion to lactoyl-CoA by a polypeptide having proprionate CoA-transferase activity classified, for example, under EC 2.8.3.1; followed by conversion to propenoyl-CoA by a polypeptide having lactoyl-CoA dehydratase activity classified, for example, under EC 4.2.1.54; followed by conversion to propanoyl-CoA by a polypeptide having butyryl-CoA dehydrogenase activity classified, for example, under EC 1.3.8.1 or a polypeptide having medium-chain acyl-CoA dehydrogenase activity classified, for example, under EC 1.3.8.7. See, e.g., FIG. 9.

In some embodiments, propanoyl-CoA is synthesized from the central metabolite, malonyl-CoA, by conversion of malonyl-CoA to malonate semialdehyde by a polypeptide having malonyl-CoA reductase activity classified, for example, under EC 1.2.1.75; followed by conversion to 3-hydroxypropionate by a polypeptide having 3-hydroxypropionate dehydrogenase activity classified, for example, under EC 1.1.1.59; followed by conversion to 3-hydroxypropionyl-CoA by a polypeptide having 3-hydroxyisobutyryl-CoA hydrolase activity classified, for example, under EC 6.2.1.- such as EC 6.2.1.36; followed by conversion to propenoyl-CoA by a polypeptide having 3-hydroxypropionyl-CoA dehydratase activity classified, for example, under EC 4.2.1.116; followed by conversion to propanoyl-CoA by a polypeptide having butyryl-CoA dehydrogenase activity classified, for example, under EC 1.3.8.1 or a polypeptide having medium-chain acyl-CoA dehydrogenase activity classified, for example, under EC 1.3.8.7. See, e.g., FIG. 9.

Pathways to Pentanoyl-CoA as Central Precursor to C5 Building Blocks

In some embodiments, pentanoyl-CoA is synthesized from propanoyl-CoA by conversion of propanoyl-CoA to 3-oxopentanoyl-CoA by a polypeptide having β-ketothiolase activity classified, for example, under EC 2.3.1.16, such as the gene product of bktB (Genbank Accession No. AAC38322.1) or classified, for example, under EC 2.3.1.174 such as the gene product of paaJ (Genbank Accession No. AAC54479.1); followed by conversion of 3-oxopentanoyl-CoA to (S) 3-hydroxybutanoyl-CoA by a polypeptide having 3-hydroxyacyl-CoA dehydrogenase activity classified, for example, under EC 1.1.1.35, such as the gene product of fadB or classified, for example, under EC 1.1.1.157 such as the gene product of hbd; followed by conversion of (S) 3-hydroxypentanoyl-CoA to pent-2-enoyl-CoA by a polypeptide having enoyl-CoA hydratase activity classified, for example, under EC 4.2.1.17 such as the gene product of crt (Genbank Accession No. AAA95967.1); followed by conversion of pent-2-enoyl-CoA to pentanoyl-CoA by a polypeptide having trans-2-enoyl-CoA reductase activity classified, for example, under EC 1.3.1.44 such as the gene product of ter (Genbank Accession No. AAW66853.1) or tdter (Genbank Accession No. AAS11092.1); followed by conversion of pentanoyl-CoA to 3-oxo-pentanoyl-CoA by a polypeptide having β-ketothiolase activity classified, for example, under EC 2.3.1.16 such as the gene product of bktB (Genbank Accession No. AAC38322.1) or classified, for example, under EC 2.3.1.174 such as the gene product of paaJ (Genbank Accession No. AAC54479.1); followed by conversion of 3-oxo-pentanoyl-CoA to (S) 3-hydroxypentanoyl-CoA by a polypeptide having 3-hydroxyacyl-CoA dehydrogenase activity classified, for example, under EC 1.1.1.35 such as the gene product of fadB or by a polypeptide having 3-hydroxyacyl-CoA dehydrogenase activity classified, for example, under EC 1.1.1.157 such as the gene product of hbd; followed by conversion of (S) 3-hydroxypentanoyl-CoA to pent-2-enoyl-CoA by a polypeptide having enoyl-CoA hydratase activity classified, for example, under EC 4.2.1.17 such as the gene product of crt (Genbank Accession No. AAA95967.1); followed by conversion of pent-2-enoyl-CoA to pentanoyl-CoA by a polypeptide having trans-2-enoyl-CoA reductase activity classified, for example, under EC 1.3.1.44 such as the gene product of ter (Genbank Accession No. AAW66853.1) or tdter (Genbank Accession No. AAS11092.1). See FIG. 1.

In some embodiments, pentanoyl-CoA is synthesized from the central metabolite, propanoyl-CoA, by conversion of propanoyl-CoA to 3-oxopentanoyl-CoA by a polypeptide having β-ketothiolase activity classified, for example, under EC 2.3.1.16, such as the gene product of bktB; followed by conversion of 3-oxopentanoyl-CoA to (R) 3-hydroxypentanoyl-CoA by a polypeptide having 3-oxoacyl-CoA reductase activity classified, for example, under EC 1.1.1.100, such as the gene product of fadG or by a polypeptide having acetoacetyl-CoA reductase activity classified, for example, under EC 1.1.1.36 such as the gene product of phaB; followed by conversion of (R) 3-hydroxypentanoyl-CoA to pent-2-enoyl-CoA by a polypeptide having enoyl-CoA hydratase activity classified, for example, under EC 4.2.1.119 such as the gene product of phaJ (Genbank Accession No. BAA21816.1); followed by conversion of pent-2enoyl-CoA to pentanoyl-CoA by a polypeptide having trans-2-enoyl-CoA reductase activity classified, for example, under EC 1.3.1.38 or a polypeptide having acyl-CoA dehydrogenase activity classified, for example, under EC 1.3.1.8; followed by conversion of pentanoyl-CoA to 3-oxo-pentanoyl-CoA by a polypeptide having β-ketothiolase activity classified, for example, under EC 2.3.1.16 such as the gene product of bktB (Genbank Accession No. AAC38322.1) or classified, for example, under EC 2.3.1.174 such as the gene product of paaJ (Genbank Accession No. AAC54479.1); followed by conversion of 3-oxo-pentanoyl-CoA to (R) 3-hydroxypentanoyl-CoA by a polypeptide having 3-oxoacyl-CoA reductase activity classified, for example, under EC 1.1.1.100 such as the gene product of fabG; followed by conversion of (R) 3-hydroxypentanoyl-CoA to pent-2-enoyl-CoA by a polypeptide having enoyl-CoA hydratase activity classified, for example, under EC 4.2.1.119 such as the gene product of phaJ (Genbank Accession No. BAA21816.1); followed by conversion of pent-2-enoyl-CoA to pentanoyl-CoA by a polypeptide having trans-2-enoyl-CoA reductase activity classified, for example, under EC 1.3.1.38 or a polypeptide having acyl-CoA dehydrogenase activity classified, for example, under EC 1.3.1.8. See FIG. 2.

In some embodiments, 3-oxopentanoyl-CoA can be synthesized from acetyl-CoA. A polypeptide having acetyl-CoA carboxylase activity classified, for example, under EC 6.4.1.2 can be used to convert acetyl-CoA to malonyl-CoA, which can be converted to 3-oxopentanoyl-CoA using a polypeptide having β-ketoacyl-[acp] synthase activity classified, for example, under EC 2.3.1.- such as EC 2.3.1.41, EC 2.3.1.179 or EC 2.3.1.180 such as the gene product of fabH. See, FIG. 1 and FIG. 2.

Pathways Using Pentanoyl-CoA to Produce the Central Precursor Pentanoate

In some embodiments, pentanoate is synthesized from pentanoyl-CoA by conversion of pentanoyl-CoA to pentanoate by a polypeptide having thioesterase activity classified, for example, under EC 3.1.2.- such as the gene product of YciA, tesB, Acot13, a Lactobacillus brevis acyl-[acp] thioesterase (GenBank Accession No. ABJ63754.1, SEQ ID NO:33) or a Lactobacillus plantarum acyl-[acp] thioesterase (GenBank Accession No. CCC58182.1, SEQ ID NO:34). See, FIG. 3.

In some embodiments, pentanoyl-CoA is converted to pentanal by a polypeptide having butanal dehydrogenase activity classified, for example, under EC 1.2.1.- such as EC 1.2.1.10 or EC 1.2.1.57 (see, e.g, GenBank Accession No. AAD39015, SEQ ID NO:30); followed by conversion of pentanal to pentanoate by a polypeptide having aldehyde dehydrogenase activity classified, for example, under EC 1.2.1.4 or EC 1.2.1.3. See FIG. 3.

The conversion of hexanoyl-CoA to hexanal has been demonstrated using both NADH and NADPH as co-factors (see Palosaari and Rogers, J. Bacteriol., 1988, 170(7): 2971-2976).

Pathways Using Pentanoyl-CoA to Produce the Central Precursor Pentanol

In some embodiments, pentanoate is synthesized from pentanoyl-CoA by conversion of pentanoyl-CoA to pentanoate by a polypeptide having thioesterase activity classified, for example, under EC 3.1.2.- such as the gene product of YciA, tesB or Acot13, a Lactobacillus brevis acyl-[acp] thioesterase (GenBank Accession No. ABJ63754.1, SEQ ID NO:33) or a Lactobacillus plantarum acyl-[acp] thioesterase (GenBank Accession No. CCC58182.1, SEQ ID NO:34); followed by conversion of pentanoate to pentanal by a polypeptide having carboxylate reductase activity classified, for example, under EC 1.2.99.6, such as the gene product of car enhanced by the gene product of sfp; followed by conversion of pentanal to pentanol by a polypeptide having alcohol dehydrogenase activity classified, for example, under EC 1.1.1.- such as EC 1.1.1.1, EC 1.1.1.2, EC 1.1.1.21, or EC 1.1.1.184) such as the gene product of YMR318C (Genbank Accession No. CAA90836.1) or YqhD (from E. coli, GenBank Accession No. AAA69178.1) (see, e.g., Liu et al., Microbiology, 2009, 155, 2078-2085; Larroy et al., 2002, Biochem J., 361(Pt 1), 163-172; or Jarboe, 2011, Appl. Microbiol. Biotechnol., 89(2), 249-257) or the protein having GenBank Accession No. CAA81612.1 (from Geobacillus stearothermophilus). See, FIG. 3.

In some embodiments, pentanoyl-CoA is converted to pentanal by a polypeptide having butanal dehydrogenase activity classified, for example, under EC 1.2.1.57 (see, e.g., GenBank Accession No. BAD61059.1, SEQ ID NO:31); followed by conversion of pentanal to pentanol by a polypeptide having alcohol dehydrogenase activity classified, for example, under EC 1.1.1.- such as EC 1.1.1.1, EC 1.1.1.2, EC 1.1.1.21, or EC 1.1.1.184) such as the gene product of YMR318C (Genbank Accession No. CAA90836.1) or YqhD (from E. coli, GenBank Accession No. AAA69178.1) (see, e.g., Liu et al., Microbiology, 2009, 155, 2078-2085; Larroy et al., 2002, Biochem J., 361(Pt 1), 163-172; or Jarboe, 2011, Appl. Microbiol. Biotechnol., 89(2), 249-257) or the protein having GenBank Accession No. CAA81612.1 (from Geobacillus stearothermophilus). See, FIG. 3.

Pathways Using Pentanoate or Pentanoyl-CoA as Central Precursor to 5-Hydroxypentanoate

In some embodiments, 5-hydroxypentanoate is synthesized from the central precursor, pentanoate, by conversion of pentanoate to pentanoate methyl ester using a polypeptide having fatty acid O-methyltransferase activity classified, for example, under EC 2.1.1.15 (e.g., the fatty acid O-methyltransferase from Mycobacterium marinum (GenBank Accession No. ACC41782.1. SEQ ID NO:23), Mycobacterium smegmatis (see GenBank Accession No. ABK73223.1, SEQ ID NO: 24), or Pseudomonas putida (see GenBank Accession No. CAA39234.1, SEQ ID NO: 25); followed by conversion to 5-hydroxypentanoate methyl ester using a polypeptide having monooxygenase activity classified, for example, under EC 1.14.14.- or EC 1.14.15.- (e.g., EC 1.14.15.1 or EC 1.14.15.3) such as a monooxygenase in the CYP153A, a CYP52A3 family, or alkB family; followed by conversion to 5-hydroxypentanoate using a polypeptide having syringate O-demethylase activity classified under EC 2.1.1.- such as the gene products of ligM (see GenBank Accession No. BAD61059.1; SEQ ID NO:31) or desA (GenBank Accession No. BAC59257.1; SEQ ID NO:32), or using a polypeptide having esterase activity classified under EC 3.1.1. such as the gene product of EstC (see GenBank Accession No. AAC60471.2, SEQ ID NO: 27) (Kim et al., 1994, Biosci. Biotech. Biochem, 58(1), 111-116).

In some embodiments, pentanoate can be enzymatically converted to 5-hydroxypentanoate by a polypeptide having monooxygenase activity (classified, for example, under EC 1.14.14.- or EC 1.14.15.- such as a monooxygenase in the CYP153A, the CYP52A3 family, and/or the gene product of alkB family.

In some embodiments, pentanoyl-CoA can be converted to pentanoic acid pentyl ester using a polypeptide having alcohol O-acetyltransferase activity classified, for example, under EC 2.3.1.-(84) such as the gene product of Eht1 (Genbank Accession No: CAA85138.1, SEQ ID NO: 25); followed by conversion to 5-hydroxypentanoic acid pentyl ester and/or 5-hydroxypentanoic acid 5-hydroxypentyl ester using a polypeptide having monooxygenase activity classified, for example, under EC 1.14.14.- or EC 1.14.15.- (1,3). For example, a polypeptide having monooxygenase activity can be, for example, from the CYP153A family, the CYP52A3 family (Genbank Accession No: BAA00371.1, SEQ ID NO: 29) or the alkB family such as the gene product of alkBGT from Pseudomonas putida (Genbank Accession No. CAB51047.1, SEQ ID NO: 28); followed by conversion of 5-hydroxypentanoic acid pentyl ester and/or 5-hydroxypentanoic acid 5-hydroxypentyl to 5-hydroxypentanoate using a polypeptide having esterase activity classified, for example, under EC 3.1.1.-(1,6) such as the gene product of EstC (see GenBank Accession No. AAC60471.2, SEQ ID NO: 27) (Kim et al., 1994, Biosci. Biotech. Biochem, 58(1), 111-116). See FIG. 7.

Pathways Using 5-Hydroxypentanoate as Central Precursor to Glutarate

Glutarate semialdehyde can be synthesized by enzymatically converting 5-hydroxypentanoate to glutarate semialdehyde using a polypeptide having alcohol dehydrogenase activity classified, for example, under EC 1.1.1.- such as the gene product of YMR318C (classified, for example, under EC 1.1.1.2, see Genbank Accession No. CAA90836.1) (Larroy et al., 2002, Biochem J., 361(Pt 1), 163-172), cpnD (Iwaki et al., 2002, Appl. Environ. Microbiol., 68(11):5671-5684) or gabD (Lütke-Eversloh & Steinbüchel, 1999, FEMS Microbiology Letters, 181(1):63-71), a polypeptide having 6-hydroxyhexanoate dehydrogenase activity classified, for example, under EC 1.1.1.258 such as the gene product of ChnD (Iwaki et al., Appl. Environ. Microbiol., 1999, 65(11):5158-5162), or a polypeptide having cytochrome P450 activity (Sanders et al., J. Lipid Research, 2005, 46(5), 1001-1008; Sanders et al., The FASEB Journal, 2008, 22(6), 2064-2071). See, FIG. 4. The polypeptide having alcohol dehydrogenase activity encoded by YMR318C has broad substrate specificity, including the oxidation of C5 alcohols.

Glutarate semialdehyde can be enzymatically converted to glutaric acid using a polypeptide having aldehyde dehydrogenase activity classified, for example, under EC 1.2.1.- (3,16,20,63,79) such as a polypeptide having 7-oxoheptanoate dehydrogenase activity (e.g., the gene product of ThnG), a polypeptide having 6-oxohexanoate dehydrogenase activity (e.g., the gene product of ChnE), or a polypeptide having aldehyde dehydrogenase activity classified under EC 1.2.1.3. See FIG. 4.

Pathway Using 5-Hydroxypentanoate as Central Precursor to 5-Aminopentanoate

In some embodiments, 5-aminopentanoate is synthesized from 5-hydroxypentanoate by conversion of 5-hydroxypentanoate to glutarate semialdehyde using a polypeptide having alcohol dehydrogenase activity classified, for example, under EC 1.1.1.- such as the gene product of YMR318C (classified, for example, under EC 1.1.1.2, see Genbank Accession No. CAA90836.1) (Larroy et al., 2002, Biochem J., 361(Pt 1), 163-172), cpnD (Iwaki et al., 2002, Appl. Environ. Microbiol., 68(11):5671-5684), or gabD (Lütke-Eversloh & Steinbüchel, 1999, FEMS Microbiology Letters, 181(1):63-71), or a polypeptide having 6-hydroxyhexanoate dehydrogenase activity classified, for example, under EC 1.1.1.258 such as the gene product of ChnD (Iwaki et al., Appl. Environ. Microbiol., 1999, 65(11):5158-5162); followed by conversion to 5-aminopentanoate by a polypeptide having ω-transaminase activity classified, for example, under EC 2.6.1.18, EC 2.6.1.19, EC 2.6.1.29, EC 2.6.1.48, EC 2.6.1.82 such as from a Chromobacterium violaceum (see Genbank Accession No. AAQ59697.1, SEQ ID NO: 7), a Pseudomonas syringae (see Genbank Accession No. AAY39893.1, SEQ ID NO: 9). See FIG. 5.

Pathway Using 5-Aminopentanoate, 5-Hydroxypentanoate, or Glutarate Semialdehyde as Central Precursor to Cadaverine

In some embodiments, cadaverine is synthesized from the central precursor 5-aminopentanoate by conversion of 5-aminopentanoate to 5-aminopentanal by a polypeptide having carboxylate reductase activity classified, for example, under EC 1.2.99.6 such as the gene product of car in combination with a phosphopantetheine transferase enhancer (e.g., encoded by a sfp gene from Bacillus subtilis or npt gene from Nocardia) or the gene products of GriC and GriD from Streptomyces griseus; followed by conversion of 5-aminopentanal to cadaverine by a polypeptide having ω-transaminase activity classified, for example, under EC 2.6.1.- such as 2.6.1.18, EC 2.6.1.19, EC 2.6.1.29, EC 2.6.1.48, or EC 2.6.1.82 such as from a Chromobacterium violaceum (see Genbank Accession No. AAQ59697.1, SEQ ID NO: 8), a Pseudomonas aeruginosa (see Genbank Accession No. AAG08191.1, SEQ ID NO: 9), a Pseudomonas syringae (see Genbank Accession No. AAY39893.1, SEQ ID NO: 10), or an Escherichia coli (see Genbank Accession No. AAA57874.1, SEQ ID NO: 12). See FIG. 6.

The polypeptide having carboxylate reductase activity encoded by the gene product of car and enhancer npt or sfp has broad substrate specificity, including terminal difunctional C4 and C5 carboxylic acids (Venkitasubramanian et al., Enzyme and Microbial Technology, 2008, 42, 130-137).

In some embodiments, cadaverine is synthesized from the central precursor 5-hydroxypentanoate (which can be produced as described in FIG. 7), by conversion of 5-hydroxypentanoate to 5-hydroxypentanal by a polypeptide having carboxylate reductase activity classified, for example, under EC 1.2.99.6 such as from a Mycobacterium marinum (see Genbank Accession No. ACC40567.1, SEQ ID NO: 2), a Mycobacterium smegmatis (see Genbank Accession No. ABK71854.1, SEQ ID NO: 3), a Segniliparus rugosus (see Genbank Accession No. EFV11917.1, SEQ ID NO: 4), a Mycobacterium massiliense (see Genbank Accession No. EIV11143.1, SEQ ID NO: 6), or a Segniliparus rotundus (see Genbank Accession No. ADG98140.1, SEQ ID NO: 7), in combination with a phosphopantetheine transferase enhancer (e.g., encoded by a sfp (Genbank Accession No. CAA44858.1, SEQ ID NO:21) gene from Bacillus subtilis or npt (Genbank Accession No. ABI83656.1, SEQ ID NO:22) gene from Nocardia), or the gene product of GriC & GriD (Suzuki et al., J. Antibiot., 2007, 60(6), 380-387); followed by conversion of 5-oxopentanol to 5-aminopentanol by a polypeptide having ω-transaminase activity classified, for example, under EC 2.6.1.- such as 2.6.1.18, EC 2.6.1.19, EC 2.6.1.29, EC 2.6.1.48, or EC 2.6.1.82 such as from a Chromobacterium violaceum (see Genbank Accession No. AAQ59697.1, SEQ ID NO: 8), a Pseudomonas syringae (see Genbank Accession No. AAY39893.1, SEQ ID NO: 10), a Rhodobacter sphaeroides (see Genbank Accession No. ABA81135.1, SEQ ID NO: 11); followed by conversion to 5-aminopentanal by a polypeptide having alcohol dehydrogenase activity classified, for example, under EC 1.1.1.- (e.g., EC 1.1.1.1, EC 1.1.1.2, EC 1.1.1.21, or EC 1.1.1.184) such as the gene product of YMR318C (Genbank Accession No. CAA90836.1) or YqhD (from E. coli, GenBank Accession No. AAA69178.1) (Liu et al., Microbiology, 2009, 155, 2078-2085; Larroy et al., 2002, Biochem J., 361(Pt 1), 163-172; Jarboe, 2011, Appl. Microbiol. Biotechnol., 89(2), 249-257) or the protein having GenBank Accession No. CAA81612.1; followed by conversion to cadaverine classified, for example, under EC 2.6.1.- such as 2.6.1.18, EC 2.6.1.19, EC 2.6.1.29, EC 2.6.1.48, or EC 2.6.1.82 such as from a Chromobacterium violaceum (see Genbank Accession No. AAQ59697.1, SEQ ID NO: 8), a Pseudomonas aeruginosa (see Genbank Accession No. AAG08191.1, SEQ ID NO: 9), a Pseudomonas syringae (see Genbank Accession No. AAY39893.1, SEQ ID NO: 10), or an Escherichia coli (see Genbank Accession No. AAA57874.1, SEQ ID NO: 12). See FIG. 6.

In some embodiments, cadaverine is synthesized from the central precursor 5-aminopentanoate by conversion of 5-aminopentanoate to N5-acetyl-5-aminopentanoate by a polypeptide having N-acetyltransferase activity such as a polypeptide having lysine N-acetyltransferase activity classified, for example, under EC 2.3.1.32; followed by conversion to N5-acetyl-5-aminopentanal by a polypeptide having carboxylate reductase activity such as from a Mycobacterium smegmatis (see Genbank Accession No. ABK71854.1, SEQ ID NO: 3), a Mycobacterium massiliense (see Genbank Accession No. EIV11143.1, SEQ ID NO: 6), or a Segniliparus rotundus (see Genbank Accession No. ADG98140.1, SEQ ID NO: 7), in combination with a phosphopantetheine transferase enhancer (e.g., encoded by a sfp (Genbank Accession No. CAA44858.1, SEQ ID NO:21) gene from Bacillus subtilis or npt (Genbank Accession No. ABI83656.1, SEQ ID NO:22) gene from Nocardia), or the gene product of GriC & GriD (Suzuki et al., J. Antibiot., 2007, 60(6), 380-387); followed by conversion to N5-acetyl-1,5-diaminopentane by a polypeptide having ω-transaminase activity such as the gene product of car in combination with a phosphopantetheine transferase enhancer (e.g., encoded by a sfp gene from Bacillus subtilis or npt gene from Nocardia) or the gene products of GriC and GriD from Streptomyces griseus; followed by conversion to cadaverine by an acetylputrescine deacetylase classified, for example, under EC 3.5.1.17 or EC 3.5.1.62. See, FIG. 6.

In some embodiments, cadaverine is synthesized from the central precursor glutarate semialdehyde by conversion of glutarate semialdehyde to pentanedial by a polypeptide having carboxylate reductase activity classified, for example, under EC 1.2.99.6 such as from a Segniliparus rotundus (see Genbank Accession No. ADG98140.1, SEQ ID NO: 7), in combination with a phosphopantetheine transferase enhancer (e.g., encoded by a sfp (Genbank Accession No. CAA44858.1, SEQ ID NO:21) gene from Bacillus subtilis or npt (Genbank Accession No. ABI83656.1, SEQ ID NO:22) gene from Nocardia), or the gene product of GriC & GriD (Suzuki et al., J. Antibiot., 2007, 60(6), 380-387); followed by conversion to 5-aminopentanal by a polypeptide having ω-transaminase activity classified, for example, under EC 2.6.1.- such as 2.6.1.18, EC 2.6.1.19, EC 2.6.1.29, EC 2.6.1.48, or EC 2.6.1.82 such as from a Chromobacterium violaceum (see Genbank Accession No. AAQ59697.1, SEQ ID NO: 8), a Pseudomonas aeruginosa (see Genbank Accession No. AAG08191.1, SEQ ID NO: 9), a Pseudomonas syringae (see Genbank Accession No. AAY39893.1, SEQ ID NO: 10), a Rhodobacter sphaeroides (see Genbank Accession No. ABA81135.1, SEQ ID NO: 11), an Escherichia coli (see Genbank Accession No. AAA57874.1, SEQ ID NO: 12), or a Vibrio fluvialis (see Genbank Accession No. AEA39183.1, SEQ ID NO: 13); followed by conversion to cadaverine by a polypeptide having ω-transaminase activity classified, for example, under EC 2.6.1.- such as 2.6.1.18, EC 2.6.1.19, EC 2.6.1.29, EC 2.6.1.48, or EC 2.6.1.82 such as from a Chromobacterium violaceum (see Genbank Accession No. AAQ59697.1, SEQ ID NO: 8), a Pseudomonas aeruginosa (see Genbank Accession No. AAG08191.1, SEQ ID NO: 9), a Pseudomonas syringae (see Genbank Accession No. AAY39893.1, SEQ ID NO: 10), or an Escherichia coli (see Genbank Accession No. AAA57874.1, SEQ ID NO: 12). See FIG. 6.

In some embodiments, cadaverine is synthesized from the central precursor 1,5-pentanediol by conversion of 1,5-pentanediol to 5-hydroxypentanal by a polypeptide having alcohol dehydrogenase activity classified, for example, under EC 1.1.1.- (e.g., EC 1.1.1.1, EC 1.1.1.2, EC 1.1.1.21, or EC 1.1.1.184) such as the gene product of YMR318C (Genbank Accession No. CAA90836.1) or YqhD (from E. coli, GenBank Accession No. AAA69178.1) (Liu et al., Microbiology, 2009, 155, 2078-2085; Larroy et al., 2002, Biochem J., 361(Pt 1), 163-172; Jarboe, 2011, Appl. Microbiol. Biotechnol., 89(2), 249-257) or the protein having GenBank Accession No. CAA81612.1; followed by conversion of 5-oxopentanal to 5-aminopentanol by a polypeptide having ω-transaminase activity classified, for example, under EC 2.6.1.- such as 2.6.1.18, EC 2.6.1.19, EC 2.6.1.29, EC 2.6.1.48, or EC 2.6.1.82 such as from a Chromobacterium violaceum (see Genbank Accession No. AAQ59697.1, SEQ ID NO: 8), a Pseudomonas aeruginosa (see Genbank Accession No. AAG08191.1, SEQ ID NO: 9), a Pseudomonas syringae (see Genbank Accession No. AAY39893.1, SEQ ID NO: 10), a Rhodobacter sphaeroides (see Genbank Accession No. ABA81135.1, SEQ ID NO: 11), an Escherichia coli (see Genbank Accession No. AAA57874.1, SEQ ID NO: 12), or a Vibrio fluvialis (see Genbank Accession No. AEA39183.1, SEQ ID NO: 13); followed by conversion to 5-aminopentanal by a polypeptide having alcohol dehydrogenase activity classified, for example, under EC 1.1.1.- (e.g., EC 1.1.1.1, EC 1.1.1.2, EC 1.1.1.21, or EC 1.1.1.184) such as the gene product of YMR318C (Genbank Accession No. CAA90836.1) or YqhD (from E. coli, GenBank Accession No. AAA69178.1) (Liu et al., Microbiology, 2009, 155, 2078-2085; Larroy et al., 2002, Biochem J., 361(Pt 1), 163-172; Jarboe, 2011, Appl. Microbiol. Biotechnol., 89(2), 249-257) or the protein having GenBank Accession No. CAA81612.1; followed by conversion to cadaverine by a polypeptide having ω-transaminase activity classified, for example, under EC 2.6.1.- such as 2.6.1.18, EC 2.6.1.19, EC 2.6.1.29, EC 2.6.1.48, or EC 2.6.1.82 such as from a Chromobacterium violaceum (see Genbank Accession No. AAQ59697.1, SEQ ID NO: 8), a Pseudomonas aeruginosa (see Genbank Accession No. AAG08191.1, SEQ ID NO: 9), a Pseudomonas syringae (see Genbank Accession No. AAY39893.1, SEQ ID NO: 10), or an Escherichia coli (see Genbank Accession No. AAA57874.1, SEQ ID NO: 12). See FIG. 6.

Pathways Using 5-Hydroxypentanoate or Pentanoyl-CoA as Central Precursor to 1,5-Pentanediol

In some embodiments, 1,5 pentanediol is synthesized from the central precursor 5-hydroxypentanoate by conversion of 5-hydroxypentanoate to 5-hydroxypentanal by a polypeptide having carboxylate reductase activity classified, for example, under EC 1.2.99.6 such as from a Mycobacterium marinum (see Genbank Accession No. ACC40567.1, SEQ ID NO: 2), a Mycobacterium smegmatis (see Genbank Accession No. ABK71854.1, SEQ ID NO: 3), a Mycobacterium smegmatis (see Genbank Accession No. ABK75684.1, SEQ ID NO: 5), a Mycobacterium massiliense (see Genbank Accession No. EIV11143.1, SEQ ID NO: 6), or a Segniliparus rotundus (see Genbank Accession No. ADG98140.1, SEQ ID NO: 7), in combination with a phosphopantetheine transferase enhancer (e.g., encoded by a sfp (Genbank Accession No. CAA44858.1, SEQ ID NO:21) gene from Bacillus subtilis or npt (Genbank Accession No. ABI83656.1, SEQ ID NO:22) gene from Nocardia), or the gene product of GriC & GriD (Suzuki et al., J. Antibiot., 2007, 60(6), 380-387); followed by conversion of 5-hydroxypentanal to 1,7 pentanediol by a polypeptide having alcohol dehydrogenase activity classified, for example, under EC 1.1.1.- such as EC 1.1.1.1, EC 1.1.1.2, EC 1.1.1.21, or EC 1.1.1.184) such as the gene product of YMR318C (Genbank Accession No. CAA90836.1) or YqhD (from E. coli, GenBank Accession No. AAA69178.1) (see, e.g., Liu et al., Microbiology, 2009, 155, 2078-2085; Larroy et al., 2002, Biochem J., 361(Pt 1), 163-172; or Jarboe, 2011, Appl. Microbiol. Biotechnol., 89(2), 249-257) or the protein having GenBank Accession No. CAA81612.1 (from Geobacillus stearothermophilus). See, FIG. 8.

In some embodiments, pentanoyl-CoA can be converted to pentanoic acid pentyl ester using a polypeptide having alcohol O-acetyltransferase activity classified, for example, under EC 2.3.1.-(84) such as the gene product of Eht1 (Genbank Accession No: CAA85138.1, SEQ ID NO: 26); followed by conversion to pentanoic acid 5-hydroxy pentyl ester and/or 5-hydroxypentanoic acid 5-hydroxypentyl ester using a polypeptide having monooxygenase activity classified, for example, under EC 1.14.14.- or EC 1.14.15.- (1,3). For example, a polypeptide having monooxygenase activity can be, for example, from the CYP153A family, the CYP52A3 (Genbank Accession No: BAA00371.1, SEQ ID NO: 29) family or the alkB family such as the gene product of alkBGT from Pseudomonas putida (Genbank Accession No. CAB51047.1, SEQ ID NO: 28); followed by conversion of pentanoic acid 5-hydroxy pentyl ester and/or 5-hydroxypentanoic acid 5-hydroxypentyl to 1,5-pentanediol using a polypeptide having esterase activity classified, for example, under EC 3.1.1.-(1,6) such as the gene product of EstC (see GenBank Accession No. AAC60471.2, SEQ ID NO: 27). See FIG. 8.

Cultivation Strategy

In some embodiments, the cultivation strategy entails achieving an aerobic, anaerobic, micro-aerobic, or mixed oxygen/denitrification cultivation condition. Enzymes characterized in vitro as being oxygen sensitive require a micro-aerobic cultivation strategy maintaining a very low dissolved oxygen concentration (See, for example, Chayabatra & Lu-Kwang, Appl. Environ. Microbiol., 2000, 66(2), 493 0 498; Wilson and Bouwer, 1997, Journal of Industrial Microbiology and Biotechnology, 18(2-3), 116-130).

In some embodiments, the cultivation strategy entails nutrient limitation such as nitrogen, phosphate or oxygen limitation.

In some embodiments, a final electron acceptor other than oxygen such as nitrates can be utilized.

In some embodiments, a cell retention strategy using, for example, ceramic membranes can be employed to achieve and maintain a high cell density during either fed-batch or continuous fermentation.

In some embodiments, the principal carbon source fed to the fermentation in the synthesis of one or more C5 building blocks can derive from biological or non-biological feedstocks.

In some embodiments, the biological feedstock can be or can derive from, monosaccharides, disaccharides, lignocellulose, hemicellulose, cellulose, lignin, levulinic acid and formic acid, triglycerides, glycerol, fatty acids, agricultural waste, condensed distillers' solubles, or municipal waste.

The efficient catabolism of crude glycerol stemming from the production of biodiesel has been demonstrated in several microorganisms such as Escherichia coli, Cupriavidus necator, Pseudomonas oleavorans, Pseudomonas putida and Yarrowia lipolytica (Lee et al., Appl. Biochem. Biotechnol., 2012, 166:1801-1813; Yang et al., Biotechnology for Biofuels, 2012, 5:13; Meijnen et al., Appl. Microbiol. Biotechnol., 2011, 90:885-893).

The efficient catabolism of lignocellulosic-derived levulinic acid has been demonstrated in several organisms such as Cupriavidus necator and Pseudomonas putida in the synthesis of 3-hydroxyvalerate via the precursor propanoyl-CoA (Jaremko and Yu, 2011, supra; Martin and Prather, J. Biotechnol., 2009, 139:61-67).

The efficient catabolism of lignin-derived aromatic compounds such as benzoate analogues has been demonstrated in several microorganisms such as Pseudomonas putida, Cupriavidus necator (Bugg et al., Current Opinion in Biotechnology, 2011, 22, 394-400; Pérez-Pantoja et al., FEMS Microbiol. Rev., 2008, 32, 736-794).

The efficient utilization of agricultural waste, such as olive mill waste water has been demonstrated in several microorganisms, including Yarrowia lipolytica (Papanikolaou et al., Bioresour. Technol., 2008, 99(7):2419-2428).

The efficient utilization of fermentable sugars such as monosaccharides and disaccharides derived from cellulosic, hemicellulosic, cane and beet molasses, cassava, corn and other agricultural sources has been demonstrated for several microorganism such as Escherichia coli, Corynebacterium glutamicum and Lactobacillus delbrueckii and Lactococcus lactis (see, e.g., Hermann et al, J. Biotechnol., 2003, 104:155-172; Wee et al., Food Technol. Biotechnol., 2006, 44(2):163-172; Ohashi et al., J. Bioscience and Bioengineering, 1999, 87(5):647-654).

The efficient utilization of furfural, derived from a variety of agricultural lignocellulosic sources, has been demonstrated for Cupriavidus necator (Li et al., Biodegradation, 2011, 22:1215-1225).

In some embodiments, the non-biological feedstock can be or can derive from natural gas, syngas, CO₂/H₂, methanol, ethanol, benzoate, non-volatile residue (NVR) or a caustic wash waste stream from cyclohexane oxidation processes, or terephthalic acid/isophthalic acid mixture waste streams.

The efficient catabolism of methanol has been demonstrated for the methylotrophic yeast Pichia pastoris.

The efficient catabolism of ethanol has been demonstrated for Clostridium kluyveri (Seedorf et al., Proc. Natl. Acad. Sci. USA, 2008, 105(6) 2128-2133).

The efficient catabolism of CO₂ and H₂, which may be derived from natural gas and other chemical and petrochemical sources, has been demonstrated for Cupriavidus necator (Prybylski et al., Energy, Sustainability and Society, 2012, 2:11).

The efficient catabolism of syngas has been demonstrated for numerous microorganisms, such as Clostridium ljungdahlii and Clostridium autoethanogenum (Köpke et al., Applied and Environmental Microbiology, 2011, 77(15):5467-5475).

The efficient catabolism of the non-volatile residue waste stream from cyclohexane processes has been demonstrated for numerous microorganisms, such as Delftia acidovorans and Cupriavidus necator (Ramsay et al., Applied and Environmental Microbiology, 1986, 52(1):152-156).

In some embodiments, the host microorganism is a prokaryote. For example, the prokaryote can be a bacterium from the genus Escherichia such as Escherichia coli; from the genus Clostridia such as Clostridium ljungdahlii, Clostridium autoethanogenum or Clostridium kluyveri; from the genus Corynebacteria such as Corynebacterium glutamicum; from the genus Cupriavidus such as Cupriavidus necator or Cupriavidus metallidurans; from the genus Pseudomonas such as Pseudomonas fluorescens, Pseudomonas putida or Pseudomonas oleavorans; from the genus Delftia such as Delftia acidovorans; from the genus Bacillus such as Bacillus subtillis; from the genus Lactobacillus such as Lactobacillus delbrueckii; or from the genus Lactococcus such as Lactococcus lactis. Such prokaryotes also can be a source of genes to construct recombinant host cells described herein that are capable of producing one or more C5 building blocks.

In some embodiments, the host microorganism is a eukaryote. For example, the eukaryote can be a filamentous fungus, e.g., one from the genus Aspergillus such as Aspergillus niger. Alternatively, the eukaryote can be a yeast, e.g., one from the genus Saccharomyces such as Saccharomyces cerevisiae; from the genus Pichia such as Pichia pastoris; or from the genus Yarrowia such as Yarrowia lipolytica; from the genus Issatchenkia such as Issathenkia orientalis; from the genus Debaryomyces such as Debaryomyces hansenii; from the genus Arxula such as Arxula adenoinivorans; or from the genus Kluyveromyces such as Kluyveromyces lactis. Such eukaryotes also can be a source of genes to construct recombinant host cells described herein that are capable of producing one or more C5 building blocks.

Metabolic Engineering

The present document provides methods involving less than all the steps described for all the above pathways. Such methods can involve, for example, one, two, three, four, five, six, seven, eight, nine, ten, eleven, twelve or more of such steps. Where less than all the steps are included in such a method, the first, and in some embodiments the only, step can be any one of the steps listed.

Furthermore, recombinant hosts described herein can include any combination of the above enzymes such that one or more of the steps, e.g., one, two, three, four, five, six, seven, eight, nine, ten, or more of such steps, can be performed within a recombinant host. This document provides host cells of any of the genera and species listed and genetically engineered to express one or more (e.g., two, three, four, five, six, seven, eight, nine, 10, 11, 12 or more) recombinant forms of any of the enzymes recited in the document. Thus, for example, the host cells can contain exogenous nucleic acids encoding enzymes catalyzing one or more of the steps of any of the pathways described herein.

In addition, this document recognizes that where enzymes have been described as accepting CoA-activated substrates, analogous enzyme activities associated with [acp]-bound substrates exist that are not necessarily in the same enzyme class.

Also, this document recognizes that where enzymes have been described accepting (R)-enantiomers of substrate, analogous enzyme activities associated with (S)-enantiomer substrates exist that are not necessarily in the same enzyme class.

This document also recognizes that where an enzyme is shown to accept a particular co-factor, such as NADPH, or co-substrate, such as acetyl-CoA, many enzymes are promiscuous in terms of accepting a number of different co-factors or co-substrates in catalyzing a particular enzyme activity. Also, this document recognizes that where enzymes have high specificity for e.g., a particular co-factor such as NADH, an enzyme with similar or identical activity that has high specificity for the co-factor NADPH may be in a different enzyme class. In addition, enzymes in a pathway that require a particular co-factor can be replaced with an enzyme that has similar or identical activity and specificity for a different co-factor. For example, one or more steps in a pathway that use an enzyme with specificity for NADH can be replaced with an enzyme having similar or identical activity and specificity for NADPH. Similarly, one or more steps in a pathway that use an enzyme with specificity for NADPH can be replaced with an enzyme having similar or identical activity and specificity for NADH.

In some embodiments, the enzymes in the pathways outlined herein are the result of enzyme engineering via non-direct or rational enzyme design approaches with aims of improving activity, improving specificity, reducing feedback inhibition, reducing repression, improving enzyme solubility, changing stereo-specificity, or changing co-factor specificity.

In some embodiments, the enzymes in the pathways outlined here can be gene dosed, i.e., overexpressed, into the resulting genetically modified organism via episomal or chromosomal integration approaches.

In some embodiments, genome-scale system biology techniques such as Flux Balance Analysis can be utilized to devise genome scale attenuation or knockout strategies for directing carbon flux to a C5 building block.

Attenuation strategies include, but are not limited to; the use of transposons, homologous recombination (double cross-over approach), mutagenesis, enzyme inhibitors and RNAi interference.

In some embodiments, fluxomic, metabolomic and transcriptomal data can be utilized to inform or support genome-scale system biology techniques, thereby devising genome scale attenuation or knockout strategies in directing carbon flux to a C5 building block.

In some embodiments, the host microorganism's tolerance to high concentrations of a C5 building block can be improved through continuous cultivation in a selective environment.

In some embodiments, the host microorganism's endogenous biochemical network can be attenuated or augmented to (1) ensure the intracellular availability of acetyl-CoA and propanoyl-CoA, (2) create a NADH or NADPH imbalance that may be balanced via the formation of one or more C5 building blocks, (3) prevent degradation of central metabolites, central precursors leading to and including one or more C5 building blocks and/or (4) ensure efficient efflux from the cell.

In some embodiments requiring intracellular availability of propanoyl-CoA for C5 building block synthesis, endogenous enzymes catalyzing the hydrolysis of propionoyl-CoA and acetyl-CoA such as short-chain length polypeptides having thioesteras activity can be attenuated in the host organism.

In some embodiments requiring the intracellular availability of propanoyl-CoA for C5 building block synthesis, endogenous enzymes consuming propanoyl-CoA to succinyl-CoA via the methylcitrate cycle such as a polypeptide having methylcitrate synthase activity can be attenuated in the host organism (Bramer & Steinbüchel, 2001, Microbiology, 147: 2203-2214).

In some embodiments requiring the intracellular availability of propanoyl-CoA via L-threonine as central metabolite for C5 building block synthesis, a feedback-resistant polypeptide having threonine deaminase activity can be genetically engineered into the host organism (Tseng et al., Microbial Cell Factories, 2010, 9:96).

In some embodiments requiring condensation of acetyl-CoA and propanoyl-CoA for C5 building block synthesis, one or more endogenous polypeptides having β-ketothiolases activity catalyzing the condensation of only acetyl-CoA to acetoacetyl-CoA such as the endogenous gene products of AtoB or phaA can be attenuated.

In some embodiments requiring the intracellular availability of acetyl-CoA for C5 building block synthesis, an endogenous polypeptide having phosphotransacetylase activity generating acetate such as pta can be attenuated (Shen et al., Appl. Environ. Microbiol., 2011, 77(9):2905-2915).

In some embodiments requiring the intracellular availability of acetyl-CoA for C5 building block synthesis, an endogenous gene in an acetate synthesis pathway encoding a polypeptide having acetate kinase activity, such as ack, can be attenuated.

In some embodiments requiring the intracellular availability of acetyl-CoA and NADH for C5 building block synthesis, an endogenous gene encoding an enzyme that catalyzes the degradation of pyruvate to lactate such as a polypeptide having lactate dehydrogenase activity encoded by IdhA can be attenuated (Shen et al., 2011, supra).

In some embodiments requiring the intracellular availability of acetyl-CoA and NADH for C5 building block synthesis, endogenous genes encoding enzymes, such as a polypeptide having menaquinol-fumarate oxidoreductase activity, that catalyze the degradation of phophoenolpyruvate to succinate such as frdBC can be attenuated (see, e.g., Shen et al., 2011, supra).

In some embodiments requiring the intracellular availability of acetyl-CoA and NADH for C5 building block synthesis, an endogenous gene encoding an enzyme that catalyzes the degradation of acetyl-CoA to ethanol such as the polypeptide having alcohol dehydrogenase activity encoded by adhE can be attenuated (Shen et al., 2011, supra).

In some embodiments, where pathways require excess NADH co-factor for C5 building block synthesis, a recombinant polypeptide having formate dehydrogenase activity can be overexpressed in the host organism (Shen et al., 2011, supra).

In some embodiments, where pathways require excess NADH or NADPH co-factor for C5 building block synthesis, a polypeptide having transhydrogenase activity dissipating the cofactor imbalance can be attenuated.

In some embodiments, an endogenous gene encoding an enzyme that catalyzes the degradation of pyruvate to ethanol such as polypeptide having pyruvate decarboxylase activity can be attenuated.

In some embodiments, an endogenous gene encoding an enzyme that catalyzes the generation of isobutanol such as a polypeptide having 2-oxoacid decarboxylase activity can be attenuated.

In some embodiments requiring the intracellular availability of acetyl-CoA for C5 building block synthesis, a recombinant polypeptide having acetyl-CoA synthetase activity such as the gene product of acs can be overexpressed in the microorganism (Satoh et al., J. Bioscience and Bioengineering, 2003, 95(4):335-341).

In some embodiments, carbon flux can be directed into the pentose phosphate cycle to increase the supply of NADPH by attenuating an endogenous polypeptide having glucose-6-phosphate isomerase activity (EC 5.3.1.9).

In some embodiments, carbon flux can be redirected into the pentose phosphate cycle to increase the supply of NADPH by overexpression a polypeptide having 6-phosphogluconate dehydrogenase activity and/or a polypeptide having transketolase activity (Lee et al., 2003, Biotechnology Progress, 19(5), 1444-1449).

In some embodiments, where pathways require excess NADPH co-factor in the synthesis of a C5 building block, a gene such as UdhA encoding a polypeptide having puridine nucleotide transhydrogenase activity can be overexpressed in the host organisms (Brigham et al., Advanced Biofuels and Bioproducts, 2012, Chapter 39, 1065-1090).

In some embodiments, where pathways require excess NADPH co-factor in the synthesis of a C5 Building Block, a recombinant polypeptide having glyceraldehyde-3-phosphate-dehydrogenase activity such as GapN can be overexpressed in the host organisms (Brigham et al., 2012, supra).

In some embodiments, where pathways require excess NADPH co-factor in the synthesis of a C5 building block, a recombinant polypeptide having malic enzyme activity such as maeA or maeB can be overexpressed in the host organisms (Brigham et al., 2012, supra).

In some embodiments, where pathways require excess NADPH co-factor in the synthesis of a C5 building block, a recombinant polypeptide having glucose-6-phosphate dehydrogenase activity such as zwf can be overexpressed in the host organisms (Lim et al., J. Bioscience and Bioengineering, 2002, 93(6), 543-549).

In some embodiments, where pathways require excess NADPH co-factor in the synthesis of a C5 building block, a recombinant polypeptide having fructose 1,6 diphosphatase activity such as fbp can be overexpressed in the host organisms (Becker et al., J. Biotechnol., 2007, 132:99-109).

In some embodiments, where pathways require excess NADPH co-factor in the synthesis of a C5 building block, endogenous polypeptide having triose phosphate isomerase activity (EC 5.3.1.1) can be attenuated.

In some embodiments, where pathways require excess NADPH co-factor in the synthesis of a C5 building block, a recombinant polypeptide having glucose dehydrogenase activity such as the gene product of gdh can be overexpressed in the host organism (Satoh et al., J. Bioscience and Bioengineering, 2003, 95(4):335-341).

In some embodiments, endogenous enzymes facilitating the conversion of NADPH to NADH can be attenuated, such as the NADH generation cycle that may be generated via inter-conversion of polypeptides having glutamate dehydrogenase activity classified under EC 1.4.1.2 (NADH-specific) and EC 1.4.1.4 (NADPH-specific).

In some embodiments, an endogenous polypeptide having glutamate dehydrogenase activity (EC 1.4.1.3) that utilizes both NADH and NADPH as co-factors can be attenuated.

In some embodiments, a membrane-bound polypeptide having cytochrome P450 activity such as CYP4F3B can be solubilized by only expressing the cytosolic domain and not the N-terminal region that anchors the P450 to the endoplasmic reticulum (see, for example, Scheller et al., J. Biol. Chem., 1994, 269(17):12779-12783).

In some embodiments, a membrane-bound polypeptide having enoyl-CoA reductase activity can be solubilized via expression as a fusion protein to a small soluble protein such as a maltose binding protein (Gloerich et al., FEBS Letters, 2006, 580, 2092-2096).

In some embodiments using hosts that naturally accumulate polyhydroxyalkanoates, the endogenous polypeptide having polyhydroxyalkanoate synthase activity can be attenuated in the host strain.

In some embodiments requiring the intracellular availability of pentanoyl-CoA for C5 building block synthesis, a recombinant polypeptide having propionyl-CoA synthetase activity such as the gene product of PrpE-RS can be overexpressed in the microorganism (Rajashekhara & Watanabe, FEBS Letters, 2004, 556:143-147).

In some embodiments, a polypeptide having L-alanine dehydrogenase activity can be overexpressed in the host to regenerate L-alanine from pyruvate as an amino donor for ω-transaminase reactions.

In some embodiments, a polypeptide having L-glutamate dehydrogenase activity, a polypeptide having L-glutamine synthetase activity, or a polypeptide having glutamate synthase activity can be overexpressed in the host to regenerate L-glutamate from 2-oxoglutarate as an amino donor for ω-transaminase reactions.

In some embodiments, enzymes such as polypeptide having pimeloyl-CoA dehydrogenase activity classified under, EC 1.3.1.62; a polypeptide having acyl-CoA dehydrogenase activity classified, for example, under EC 1.3.8.7 or EC 1.3.8.1; and/or a polypeptide having glutaryl-CoA dehydrogenase activity classified, for example, under EC 1.3.8.6 that degrade central metabolites and central precursors leading to and including C5 building blocks can be attenuated.

In some embodiments, endogenous enzymes activating C5 building blocks via Coenzyme A esterification such as polypeptides having CoA-ligase activity (e.g., a pimeloyl-CoA synthetase) classified under, for example, EC 6.2.1.14 can be attenuated.

In some embodiments, the efflux of a C5 building block across the cell membrane to the extracellular media can be enhanced or amplified by genetically engineering structural modifications to the cell membrane or increasing any associated transporter activity for a C5 building block.

The efflux of cadaverine can be enhanced or amplified by overexpressing broad substrate range multidrug transporters such as Bit from Bacillus subtilis (Woolridge et al., 1997, J. Biol. Chem., 272(14):8864-8866); AcrB and AcrD from Escherichia coli (Elkins & Nikaido, 2002, J. Bacteriol., 184(23), 6490-6499), NorA from Staphylococcus aereus (Ng et al., 1994, Antimicrob Agents Chemother, 38(6), 1345-1355), or Bmr from Bacillus subtilis (Neyfakh, 1992, Antimicrob Agents Chemother, 36(2), 484-485).

The efflux of 5-aminopentanoate and cadaverine can be enhanced or amplified by overexpressing the solute transporters such as the lysE transporter from Corynebacterium glutamicum (Bellmann et al., 2001, Microbiology, 147, 1765-1774).

The efflux of glutaric acid can be enhanced or amplified by overexpressing a dicarboxylate transporter such as the SucE transporter from Corynebacterium glutamicum (Huhn et al., Appl. Microbiol. & Biotech., 89(2), 327-335).

Producing C5 Building Blocks Using a Recombinant Host

Typically, one or more C5 building blocks can be produced by providing a host microorganism and culturing the provided microorganism with a culture medium containing a suitable carbon source as described above. In general, the culture media and/or culture conditions can be such that the microorganisms grow to an adequate density and produce a C5 building block efficiently. For large-scale production processes, any method can be used such as those described elsewhere (Manual of Industrial Microbiology and Biotechnology, 2^(nd) Edition, Editors: A. L. Demain and J. E. Davies, ASM Press; and Principles of Fermentation Technology, P. F. Stanbury and A. Whitaker, Pergamon). Briefly, a large tank (e.g., a 100 gallon, 200 gallon, 500 gallon, or more tank) containing an appropriate culture medium is inoculated with a particular microorganism. After inoculation, the microorganism is incubated to allow biomass to be produced. Once a desired biomass is reached, the broth containing the microorganisms can be transferred to a second tank. This second tank can be any size. For example, the second tank can be larger, smaller, or the same size as the first tank. Typically, the second tank is larger than the first such that additional culture medium can be added to the broth from the first tank. In addition, the culture medium within this second tank can be the same as, or different from, that used in the first tank.

Once transferred, the microorganisms can be incubated to allow for the production of a C5 building block. Once produced, any method can be used to isolate C5 building blocks. For example, C5 building blocks can be recovered selectively from the fermentation broth via adsorption processes. In the case of glutaric acid and 5-aminopentanoic acid, the resulting eluate can be further concentrated via evaporation, crystallized via evaporative and/or cooling crystallization, and the crystals recovered via centrifugation. In the case of cadaverine and 1,5-pentanediol, distillation may be employed to achieve the desired product purity.

The invention is further described in the following examples, which do not limit the scope of the invention described in the claims.

EXAMPLES Example 1 Enzyme Activity of ω-Transaminase Using Glutarate Semialdehyde as Substrate and Forming 5-Aminopentanoate

A nucleotide sequence encoding an N-terminal His-tag was added to the genes from Chromobacterium violaceum and Rhodobacter sphaeroides encoding the ω-transaminases of SEQ ID NOs: 8 and 10 respectively (see FIG. 10) such that N-terminal HIS tagged ω-transaminases could be produced. Each of the resulting modified genes was cloned into a pET21a expression vector under control of the T7 promoter and each expression vector was transformed into a BL21[DE3] E. coli host. The resulting recombinant E. coli strains were cultivated at 37° C. in a 250 mL shake flask culture containing 50 mL LB media and antibiotic selection pressure, with shaking at 230 rpm. Each culture was induced overnight at 16 OC using 1 mM IPTG.

The pellet from each induced shake flask culture was harvested via centrifugation. Each pellet was resuspended and lysed via sonication. The cell debris was separated from the supernatant via centrifugation and the cell free extract was used immediately in enzyme activity assays.

Enzyme activity assays in the reverse direction (i.e., 5-aminopentanoate to glutarate semialdehyde) were performed in a buffer composed of a final concentration of 50 mM HEPES buffer (pH=7.5), 10 mM 5-aminopentanoate, 10 mM pyruvate and 100 μM pyridoxyl 5′ phosphate. Each enzyme activity assay reaction was initiated by adding cell free extract of the ω-transaminase gene product or the empty vector control to the assay buffer containing the 5-aminopentanoate and incubated at 25° C. for 4 h, with shaking at 250 rpm. The formation of L-alanine from pyruvate was quantified via RP-HPLC.

Each enzyme only control without 5-aminopentanoate demonstrated low base line conversion of pyruvate to L-alanine. See FIG. 17. The gene product of SEQ ID NO 8, accepted 5-aminopentanote as substrate as confirmed against the empty vector control. See FIG. 18.

Enzyme activity in the forward direction (i.e., glutarate semialdehyde to 5-aminopentanoate) was confirmed for the transaminase of SEQ ID NO 10. Enzyme activity assays were performed in a buffer composed of a final concentration of 50 mM HEPES buffer (pH=7.5), 10 mM glutarate semialdehyde, 10 mM L-alanine and 100 μM pyridoxyl 5′ phosphate. Each enzyme activity assay reaction was initiated by adding a cell free extract of the ω-transaminase gene product or the empty vector control to the assay buffer containing the glutarate semialdehyde and incubated at 25° C. for 4 h, with shaking at 250 rpm. The formation of pyruvate was quantified via RP-HPLC.

The gene product of SEQ ID NO 10 accepted glutarate semialdehyde as substrate as confirmed against the empty vector control. See FIG. 19. The reversibility of the ω-transaminase activity was confirmed, demonstrating that the ω-transaminases of SEQ ID NO 8, and SEQ ID NO 10 accepted glutarate semialdehyde as substrate and synthesized 5-aminopentanoate as a reaction product.

Example 2 Enzyme Activity of Carboxylate Reductase Using 5-Hydroxypentanoate as Substrate and Forming 5-Hydroxypentanal

A nucleotide sequence encoding a His-tag was added to the genes from Mycobacterium marinum, Mycobacterium smegmatis, Segniliparus rugosus, Mycobacterium massiliense, and Segniliparus rotundus that encode the carboxylate reductases of SEQ ID NOs: 2-4, 6 and 7, respectively (GenBank Accession Nos. ACC40567.1, ABK71854.1, EFV11917.1, EIV11143.1, and ADG98140.1, respectively) (see FIG. 10) such that N-terminal HIS tagged carboxylate reductases could be produced. Each of the modified genes was cloned into a pET Duet expression vector alongside a sfp gene encoding a His-tagged phosphopantetheine transferase from Bacillus subtilis, both under control of the T7 promoter. Each expression vector was transformed into a BL21[DE3] E. coli host along with the expression vectors from Example 3. Each resulting recombinant E. coli strain was cultivated at 37° C. in a 250 mL shake flask culture containing 50 mL LB media and antibiotic selection pressure, with shaking at 230 rpm. Each culture was induced overnight at 37° C. using an auto-induction media.

The pellet from each induced shake flask culture was harvested via centrifugation. Each pellet was resuspended and lysed via sonication. The cell debris was separated from the supernatant via centrifugation. The carboxylate reductases and phosphopantetheine transferase were purified from the supernatant using Ni-affinity chromatography, diluted 10-fold into 50 mM HEPES buffer (pH=7.5) and concentrated via ultrafiltration.

Enzyme activity (i.e., 5-hydroxypentanoate to 5-hydroxypentanal) assays were performed in triplicate in a buffer composed of a final concentration of 50 mM HEPES buffer (pH=7.5), 2 mM 5-hydroxypentanal, 10 mM MgCl₂, 1 mM ATP, and 1 mM NADPH. Each enzyme activity assay reaction was initiated by adding purified carboxylate reductase and phosphopantetheine transferase or the empty vector control to the assay buffer containing the 5-hydroxypentanoate and then incubated at room temperature for 20 min. The consumption of NADPH was monitored by absorbance at 340 nm. Each enzyme only control without 5-hydroxypentanoate demonstrated low base line consumption of NADPH. See FIG. 12.

The gene products of SEQ ID NOs: 2-4, 6 and 7, enhanced by the gene product of sfp, accepted 5-hydroxypentanoate as substrate as confirmed against the empty vector control (see FIG. 14), and synthesized 5-hydroxypentanal.

Example 3 Enzyme Activity of ω-Transaminase for 5-Aminopentanol, Forming 5-Oxopentanol

A nucleotide sequence encoding an N-terminal His-tag was added to the Chromobacterium violaceum, Pseudomonas aeruginosa, Pseudomonas syringae, Rhodobacter sphaeroide, Escherichia coli and Vibrio fluvialis genes encoding the ω-transaminases of SEQ ID NOs: 8-13, respectively (see FIG. 10) such that N-terminal HIS tagged ω-transaminases could be produced. The modified genes were cloned into a pET21a expression vector under the T7 promoter. Each expression vector was transformed into a BL21[DE3] E. coli host. Each resulting recombinant E. coli strain were cultivated at 37° C. in a 250 mL shake flask culture containing 50 mL LB media and antibiotic selection pressure, with shaking at 230 rpm. Each culture was induced overnight at 16° C. using 1 mM IPTG.

The pellet from each induced shake flask culture was harvested via centrifugation. Each pellet was resuspended and lysed via sonication. The cell debris was separated from the supernatant via centrifugation and the cell free extract was used immediately in enzyme activity assays.

Enzyme activity assays in the reverse direction (i.e., 5-aminopentanol to 5-oxopentanol) were performed in a buffer composed of a final concentration of 50 mM HEPES buffer (pH=7.5), 10 mM 5-aminopentanol, 10 mM pyruvate, and 100 μM pyridoxyl 5′ phosphate. Each enzyme activity assay reaction was initiated by adding cell free extract of the ω-transaminase gene product or the empty vector control to the assay buffer containing the 5-aminopentanol and then incubated at 25° C. for 4 h, with shaking at 250 rpm. The formation of L-alanine was quantified via RP-HPLC.

Each enzyme only control without 5-aminopentanol had low base line conversion of pyruvate to L-alanine. See FIG. 17.

The gene products of SEQ ID NOs: 8-13 accepted 5-aminopentanol as substrate as confirmed against the empty vector control (see FIG. 13) and synthesized 5-oxopentanol as reaction product. Given the reversibility of the ω-transaminase activity (see Example 1), it can be concluded that the gene products of SEQ ID NOs: 8-13 accept 5-oxopentanol as substrate and form 5-aminopentanol.

Example 4 Enzyme Activity of ω-Transaminase Using Cadaverine as Substrate and Forming 5-Aminopentanal

A nucleotide sequence encoding an N-terminal His-tag was added to the Chromobacterium violaceum, Pseudomonas aeruginosa, Pseudomonas syringae, and Escherichia coli genes encoding the ω-transaminases of SEQ ID NOs: 8-10 and 12, respectively (see FIG. 10) such that N-terminal HIS tagged ω-transaminases could be produced. The modified genes were cloned into a pET21a expression vector under the T7 promoter. Each expression vector was transformed into a BL21[DE3] E. coli host. Each resulting recombinant E. coli strain were cultivated at 37° C. in a 250 mL shake flask culture containing 50 mL LB media and antibiotic selection pressure, with shaking at 230 rpm. Each culture was induced overnight at 16° C. using 1 mM IPTG.

The pellet from each induced shake flask culture was harvested via centrifugation. Each pellet was resuspended and lysed via sonication. The cell debris was separated from the supernatant via centrifugation and the cell free extract was used immediately in enzyme activity assays.

Enzyme activity assays in the reverse direction (i.e., cadaverine to 5-aminopentanal) were performed in a buffer composed of a final concentration of 50 mM HEPES buffer (pH=7.5), 10 mM cadaverine, 10 mM pyruvate, and 100 μM pyridoxyl 5′ phosphate. Each enzyme activity assay reaction was initiated by adding cell free extract of the ω-transaminase gene product or the empty vector control to the assay buffer containing the cadaverine and then incubated at 25° C. for 4 h, with shaking at 250 rpm. The formation of L-alanine was quantified via RP-HPLC.

Each enzyme only control without cadaverine had low base line conversion of pyruvate to L-alanine. See FIG. 17.

The gene products of SEQ ID NOs: 8-10 and 12 accepted cadaverine as substrate as confirmed against the empty vector control (see FIG. 20) and synthesized 5-aminopentanal as reaction product. Given the reversibility of the ω-transaminase activity (see Example 1), it can be concluded that the gene products of SEQ ID NOs: 8-10 and 12 accept 5-aminopentanal as substrate and form cadaverine.

Example 5 Enzyme Activity of ω-Transaminase Using N5-Acetyl-1,5-Diaminopentane, and Forming N5-Acetyl-5-Aminopentanal

The activity of the N-terminal His-tagged ω-transaminases of SEQ ID NOs: 8, 10-13 (see Example 3, and FIG. 10) for converting N5-acetyl-1,5-diaminopentane to N5-acetyl-5-aminopentanal was assayed using a buffer composed of a final concentration of 50 mM HEPES buffer (pH=7.5), 10 mM N5-acetyl-1,5-diaminopentane, 10 mM pyruvate and 100 μM pyridoxyl 5′ phosphate. Each enzyme activity assay reaction was initiated by adding a cell free extract of the ω-transaminase or the empty vector control to the assay buffer containing the N5-acetyl-1,5-diaminopentane then incubated at 25° C. for 4 h, with shaking at 250 rpm. The formation of L-alanine was quantified via RP-HPLC.

Each enzyme only control without N5-acetyl-1,5-diaminopentane demonstrated low base line conversion of pyruvate to L-alanine. See FIG. 17.

The gene product of SEQ ID NOs: 8, 10 accepted N5-acetyl-1,5-diaminopentane as substrate as confirmed against the empty vector control (see FIG. 15) and synthesized N5-acetyl-5-aminopentanal as reaction product.

Given the reversibility of the ω-transaminase activity (see Example 1), the gene products of SEQ ID NOs: 8, 10 accept N5-acetyl-5-aminopentanal as substrate forming N5-acetyl-1,5-diaminopentane.

Example 6 Enzyme Activity of Carboxylate Reductase Using Glutarate Semialdehyde as Substrate and Forming Pentanedial

The N-terminal His-tagged carboxylate reductase of SEQ ID NO 7 (see Example 3 and FIG. 10) was assayed using glutarate semialdehyde as substrate. The enzyme activity assay was performed in triplicate in a buffer composed of a final concentration of 50 mM HEPES buffer (pH=7.5), 2 mM glutarate semialdehyde, 10 mM MgCl₂, 1 mM ATP and 1 mM NADPH. The enzyme activity assay reaction was initiated by adding purified carboxylate reductase and phosphopantetheine transferase or the empty vector control to the assay buffer containing the glutarate semialdehyde and then incubated at room temperature for 20 min. The consumption of NADPH was monitored by absorbance at 340 nm. The enzyme only control without glutarate semialdehyde demonstrated low base line consumption of NADPH. See FIG. 12.

The gene product of SEQ ID NO 7, enhanced by the gene product of sfp, accepted glutarate semialdehyde as substrate as confirmed against the empty vector control (see FIG. 16) and synthesized pentanedial.

Example 7 Enzyme Activity of Carboxylate Reductase Using Pentanoate as Substrate in Forming Pentanal

The N-terminal His-tagged carboxylate reductase of SEQ ID NOs 2, 3, 6 and 7 (see Example 3 and FIG. 10) was assayed using glutarate semialdehyde as substrate. The enzyme activity assay was performed in triplicate in a buffer composed of a final concentration of 50 mM HEPES buffer (pH=7.5), 2 mM pentanoate, 10 mM MgCl₂, 1 mM ATP and 1 mM NADPH. The enzyme activity assay reaction was initiated by adding purified carboxylate reductase and phosphopantetheine transferase or the empty vector control to the assay buffer containing the pentanoate and then incubated at room temperature for 20 min. The consumption of NADPH was monitored by absorbance at 340 nm. The enzyme only control without pentanoate demonstrated low base line consumption of NADPH. See FIG. 12.

The gene products of SEQ ID NOs 2, 3, 6 and 7, enhanced by the gene product of sfp, accepted pentanoate as substrate as confirmed against the empty vector control (see FIG. 11) and synthesized pentanal.

Other Embodiments

It is to be understood that while the invention has been described in conjunction with the detailed description thereof, the foregoing description is intended to illustrate and not limit the scope of the invention, which is defined by the scope of the appended claims. Other aspects, advantages, and modifications are within the scope of the following claims. 

1. A method of producing a terminal hydroxyl (C₃₋₈ hydroxyalkyl)-C(═O)OCH₃ ester in a recombinant host, said method comprising: a) enzymatically converting a C₄₋₉ carboxylic acid to a (C₃₋₈ alkyl)-C(═O)OCH₃ ester using a polypeptide having fatty acid O-methyltransferase activity, said polypeptide having fatty acid O-methyltransferase activity having at least 70% sequence identity to an amino acid sequence set forth in SEQ ID NO:23, SEQ ID NO:24, or SEQ ID NO:25; and b) enzymatically converting the (C₃₋₈ alkyl)-C(═O)OCH₃ ester to terminal hydroxyl (C₃₋₈ hydroxyalkyl)-C(═O)OCH₃ ester using a polypeptide having monooxygenase activity, wherein said polypeptide having monooxygenase activity is classified under EC 1.14.14.- or EC 1.14.15.- and has at least 70% sequence identity to an amino acid sequence set forth in SEQ ID NO: 14, SEQ ID NO: 15, SEQ ID NO: 16, SEQ ID NO:28, or SEQ ID NO:29, the method optionally further comprising enzymatically converting the terminal hydroxyl (C₃₋₈ hydroxyalkyl)-C(═O)OCH₃ ester to a terminal hydroxyl C₄₋₉ hydroxyalkanoate.
 2. (canceled)
 3. (canceled)
 4. (canceled)
 5. (canceled)
 6. (canceled)
 7. The method of claim 1, wherein the C₄₋₉ carboxylic acid is enzymatically produced from a C₄₋₉ alkanoyl-CoA using: a polypeptide having thioesterase activity, wherein said polypeptide having thioesterase activity has at least 70% sequence identity to the amino acid sequence set forth in SEQ ID NO:1, SEQ ID NO: 33, or SEQ ID NO: 34; or a polypeptide having butanal dehydrogenase activity and a polypeptide having aldehyde dehydrogenase activity.
 8. (canceled)
 9. (canceled)
 10. (canceled)
 11. (canceled)
 12. The method of claim 1, wherein a polypeptide having demethylase activity or a polypeptide having esterase activity enzymatically converts the terminal hydroxyl (C₃₋₈ hydroxyalkyl)-C(═O)OCH₃ ester to a terminal hydroxyl C₄₋₉ hydroxyalkanoate.
 13. The method of claim 1, wherein the C₄₋₉ carboxylic acid is pentanoate, and is enzymatically converted to pentanoate methyl ester; and the pentanoate methyl ester is enzymatically converted to 5-hydroxypentanoate methyl ester, the method optionally further comprising enzymatically converting 5-hydroxypentanoate methyl ester to 5-hydroxypentanoate using a polypeptide having demethylase or esterase activity.
 14. The method of claim 7, wherein the C₄₋₉ alkanoyl-CoA is pentanoyl-CoA and pentanoate is enzymatically produced from pentanoyl-CoA.
 15. A method of producing one or more terminal hydroxy-substituted (C₄₋₉ alkyl)-OC(═O)—(C₃₋₈ alkyl) esters in a recombinant host, said method comprising: a) enzymatically converting a C₄₋₉ alkanoyl-CoA to a (C₄₋₉ alkyl)-OC(═O)—(C₃₋₈ alkyl) ester in said host using a polypeptide having alcohol O-acetyltransferase activity, wherein said polypeptide having alcohol O-acetyltransferase activity has at least 70% sequence identity to the amino acid sequence set forth in SEQ ID NO: 26; and b) enzymatically converting the (C₄₋₉ alkyl)-OC(═O)—(C₃₋₈ alkyl) ester to any of (C₄₋₉ alkyl)-OC(═O)—(C₃₋₈ hydroxyalkyl) ester, (C₄₋₉ hydroxyalkyl)-OC(═O)—(C₃₋₈ hydroxyalkyl) ester, or (C₄₋₉ hydroxyalkyl)-OC(═O)—(C₃₋₈ alkyl) ester in said host the method optionally further comprising enzymatically converting (C₄₋₉ hydroxyalkyl)-OC(═O)—(C₃₋₈ hydroxyalkyl) ester or (C₄₋₉ hydroxyalkyl)-OC(═O)—(C₃₋₈ alkyl) ester to a terminal hydroxyl C₄₋₉ hydroxyalkanoate, said enzymatic conversion using a polypeptide having esterase activity enzymatically converts (C₄₋₉ hydroxyalkyl)-OC(═O)—(C₃₋₈ hydroxyalkyl) ester or (C₄₋₉ hydroxyalkyl)-OC(═O)—(C₃₋₈ alkyl) ester to the C₄₋₉ hydroxyalkanoate.
 16. (canceled)
 17. (canceled)
 18. The method of claim 15, wherein (C₄₋₉ alkyl)-OC(═O)—(C₃₋₈ alkyl) ester is enzymatically converted to any of (C₄₋₉ alkyl)-OC(═O)—(C₃₋₈ hydroxyalkyl) ester, (C₄₋₉ hydroxyalkyl)-OC(═O)—(C₃₋₈ hydroxyalkyl) ester, or (C₄₋₉ hydroxyalkyl)-OC(═O)—(C₃₋₈ alkyl) ester using a polypeptide having monooxygenase activity, wherein said polypeptide having monooxygenase activity is classified under EC 1.14.14.- or EC 1.14.15.- and has at least 70% sequence identity to an amino acid sequence set forth in SEQ ID NO: 14, SEQ ID NO: 15, SEQ ID NO: 16, SEQ ID NO:28, or SEQ ID NO:29.
 19. (canceled)
 20. (canceled)
 21. (canceled)
 22. (canceled)
 23. The method of claim 15, wherein the C₄₋₉ alkanoyl-CoA is pentanoyl-CoA and is enzymatically converted to pentanoic acid pentyl ester; and pentanoic acid pentyl ester is enzymatically converted to any of 5-hydroxypentanoic acid pentyl ester, 5-hydroxypentanoic acid 5-hydroxypentyl ester, or pentanoic acid 5-hydroxypentyl ester using a polypeptide having monooxygenase activity, the method optionally further comprising enzymatically converting 5-hydroxypentanoic acid 5-hydroxypentyl ester or 5-hydroxypentanoic acid pentyl ester to 5-hydroxypentanoate, said enzymatic conversion of 5-hydroxypentanoic acid 5-hydroxypentyl ester or 5-hydroxypentanoic acid pentyl ester to 5-hydroxypentanoate using a polypeptide having esterase activity.
 24. (canceled)
 25. (canceled)
 26. The method of claim 23, said method further comprising enzymatically converting 5-hydroxypentanoic acid 5-hydroxypentyl ester or pentanoic acid 5-hydroxypentyl ester to 1,5-pentanediol, said enzymatic conversion of 5-hydroxypentanoic acid 5-hydroxypentyl ester or pentanoic acid 5-hydroxypentyl ester to 1,5-pentanediol using a polypeptide having esterase activity, the method optionally further comprising enzymatically converting 1,5-pentanediol to 5-hydroxypentanoate using a polypeptide having alcohol dehydrogenase activity and a polypeptide having aldehyde dehydrogenase activity.
 27. (canceled)
 28. (canceled)
 29. (canceled)
 30. (canceled)
 31. (canceled)
 32. The method of claim 23, said method further comprising enzymatically converting 5-hydroxypentanoate to a product selected from the group consisting of glutaric acid, glutarate semialdehyde, 5-aminopentanoate, cadaverine, and 1,5-pentanediol, said enzymatic conversion of 5-hydroxypentanoate to glutarate semialdehyde using: a polypeptide having alcohol dehydrogenase activity, a polypeptide having 6-hydroxyhexanoate dehydrogenase activity, a polypeptide having 5-hydroxypentanoate dehydrogenase activity, a polypeptide having 4-hydroxybutyrate dehydrogenase activity, or a polypeptide having monooxygenase activity, the method optionally further comprising enzymatically converting glutarate semialdehyde to glutaric acid using a polypeptide having 7-oxoheptanoate dehydrogenase activity, a polypeptide having 6-oxohexanoate dehydrogenase activity, a polypeptide having 5-oxopentanoate dehydrogenase activity, a polypeptide having aldehyde dehydrogenase activity, or a polypeptide having monooxygenase activity.
 33. (canceled)
 34. (canceled)
 35. The method of claim 32, said method further comprising enzymatically converting glutarate semialdehyde to 5-aminopentanoate using a polypeptide having ω-transaminase activity, wherein said polypeptide having ω-transaminase activity has at least 70% sequence identity to any one of the amino acid sequences set forth in SEQ ID NO. 8-13, the method optionally further comprising enzymatically converting 5-aminopentanoate to cadaverine.
 36. (canceled)
 37. (canceled)
 38. The method of claim 32, said method further comprising enzymatically converting glutarate semialdehyde to heptamethylenediamine.
 39. The method of claim 35, wherein glutarate semialdehyde or 5-aminopentanoate is enzymatically converted to cadaverine using a polypeptide having carboxylate reductase activity and/or a polypeptide having ω-transaminase activity, and optionally one or more of a polypeptide having N-acetyl transferase activity, a polypeptide having acetylputrescine deacetylase activity, and a polypeptide having alcohol dehydrogenase activity.
 40. The method of claim 39, wherein the polypeptide having carboxylate reductase is enhanced by the gene product of sfp.
 41. The method of claim 39, wherein 5-hydroxypentanoate is enzymatically converted to 1,5-pentanediol using a polypeptide having carboxylate reductase activity and a polypeptide having alcohol dehydrogenase activity, the method optionally further comprising enzymatically converting 1,5-pentanediol to cadaverine using a polypeptide having alcohol dehydrogenase activity and a polypeptide having ω-transaminase activity.
 42. (canceled)
 43. (canceled)
 44. The method of claim 32, wherein a polypeptide having carboxylate reductase activity, a polypeptide having ω-transaminase activity, and a polypeptide having alcohol dehydrogenase activity enzymatically convert 5-hydroxypentanoate to cadaverine.
 45. (canceled)
 46. The method of claim 14, wherein pentanoyl-CoA is produced from acetyl-CoA and propanoyl-CoA via two cycles of CoA-dependent carbon chain elongation, wherein each of said two cycles of CoA-dependent carbon chain elongation comprises using (i) a polypeptide having β-ketothiolase activity or a polypeptide having acetyl-CoA carboxylase activity and a polypeptide having β-ketoacyl-[acp] synthase activity, (ii) a polypeptide having 3-hydroxyacyl-CoA dehydrogenase activity or a polypeptide having 3-oxoacyl-CoA reductase activity, (iv) a polypeptide having enoyl-CoA hydratase activity, and (v) a polypeptide having trans-2-enoyl-CoA reductase activity to form pentanoyl-CoA from acetyl-CoA and propanoyl-CoA.
 47. (canceled)
 48. A method of enzymatically producing 5-hydroxypentanoate, the method comprising: a) enzymatically converting pentanoate to pentanoate methyl ester using a polypeptide having fatty acid O-methyltransferase activity; b) enzymatically converting heptanoate methyl ester to 5-hydroxypentanoate methyl ester using a polypeptide having monooxygenase activity; and c) enzymatically converting 5-hydroxypentanoate methyl ester to 5-hydroxypentanoate using a polypeptide having demethylase activity or a polypeptide having esterase activity.
 49. A method of enzymatically producing 5-hydroxypentanoate, the method comprising: a) enzymatically converting pentanoyl-CoA to pentanoic acid pentyl ester using a polypeptide having alcohol O-acetyltransferase activity; b) enzymatically converting pentanoic acid pentyl ester to 5-hydroxypentanoic acid pentyl ester, pentanoic acid 5-hydroxypentyl ester or 5-hydroxypentanoic acid 5-hydroxypentyl ester using a polypeptide having monooxygenase activity; and c) enzymatically converting 5-hydroxypentanoic acid pentyl ester, pentanoic acid 5-hydroxypentyl ester or 5-hydroxypentanoic acid 5-hydroxypentyl ester to 5-hydroxypentanoate using a polypeptide having esterase activity.
 50. The method of claim 1, wherein said recombinant host is subjected to a cultivation strategy under aerobic, anaerobic or, micro-aerobic cultivation conditions.
 51. The method of claim 50, wherein said recombinant host is cultured under conditions of nutrient limitation, such as phosphate, nitrogen and oxygen limitation.
 52. The method of claim 50, wherein said recombinant host is retained using a ceramic membrane to maintain a high cell density during fermentation.
 53. The method of claim 50, wherein the principal carbon source fed to the recombinant host derives from a biological feedstock.
 54. The method of claim 53, wherein the biological feedstock is, or derives from, monosaccharides, disaccharides, lignocellulose, hemicellulose, cellulose, lignin, levulinic acid, formic acid, triglycerides, glycerol, fatty acids, agricultural waste, condensed distillers' solubles, or municipal waste.
 55. The method of claim 50 wherein the principal carbon source fed to the recombinant host derives from a non-biological feedstock.
 56. The method of claim 55, wherein the non-biological feedstock is, or derives from, natural gas, syngas, CO₂/H₂, methanol, ethanol, benzoate, non-volatile residue (NVR) caustic wash waste stream from cyclohexane oxidation processes, or terephthalic acid/isophthalic acid mixture waste streams.
 57. The method of claim 50, wherein the recombinant host is a prokaryote selected from the group consisting of Escherichia; Clostridia; Corynebacteria; Cupriavidus; Pseudomonas; Delftia; Bacillus; Lactobacillus; Lactococcus; and Rhodococcus, or a eukaryote selected from the group consisting of Aspergillus, Saccharomyces, Pichia, Yarrowia, Issatchenkia, Debaryomyces, Arxula, and Kluyveromyces.
 58. (canceled)
 59. (canceled)
 60. (canceled)
 61. (canceled)
 62. (canceled)
 63. The method of claim 50, wherein said recombinant host comprises one or more of the following attenuated enzymes: a polypeptide having polyhydroxyalkanoate synthase activity, a polypeptide having acetyl-CoA thioesterase activity, a polypeptide having propanoyl-CoA thioesterase activity, a polypeptide having phosphotransacetylase forming acetate activity, a polypeptide having acetate kinase activity, a polypeptide having lactate dehydrogenase activity, a polypeptide having menaquinol-fumarate oxidoreductase activity, a polypeptide having 2-oxoacid decarboxylase activity producing isobutanol, a polypeptide having alcohol dehydrogenase activity forming ethanol, a polypeptide having triose phosphate isomerase activity, a polypeptide having pyruvate decarboxylase activity, a polypeptide having glucose-6-phosphate isomerase activity, a polypeptide having transhydrogenase activity dissipating the cofactor gradient, a polypeptide having glutamate dehydrogenase activity specific for the cofactor gradient, a NADH/NADPH-utilizing polypeptide having glutamate dehydrogenase activity, a polypeptide having pimeloyl-CoA dehydrogenase activity; a polypeptide having acyl-CoA dehydrogenase activity accepting C5 building blocks and central precursors as substrates; a polypeptide having glutaryl-CoA dehydrogenase activity; or a polypeptide having pimeloyl-CoA synthetase activity.
 64. The method of claim 50, wherein said recombinant host overexpresses one or more genes encoding: a polypeptide having acetyl-CoA synthetase activity, a polypeptide having propionate-CoA synthetase activity, a polypeptide having 6-phosphogluconate dehydrogenase activity; a polypeptide having transketolase activity; a polypeptide having puridine nucleotide transhydrogenase activity; a polypeptide having formate dehydrogenase activity; a polypeptide having glyceraldehyde-3P-dehydrogenase activity; a polypeptide having malic enzyme activity; a polypeptide having glucose-6-phosphate dehydrogenase activity; a polypeptide having fructose 1,6 diphosphatase activity; a polypeptide having L-alanine dehydrogenase activity; a polypeptide having L-glutamate dehydrogenase activity; a polypeptide having L-glutamine synthetase activity; a polypeptide having lysine transporter activity; a polypeptide having dicarboxylate transporter activity; and/or a polypeptide having multidrug transporter activity.
 65. A recombinant host comprising at least one exogenous nucleic acid encoding (i) a polypeptide having fatty acid O-methyltransferase activity and (ii) a polypeptide having monooxygenase activity, said recombinant host producing a terminal hydroxyl (C₃₋₈ hydroxyalkyl)-C(═O)OCH₃ ester, wherein said polypeptide having fatty acid O-methyltransferase activity has at least 70% sequence identity to an amino acid sequence set forth in SEQ ID NO:23, SEQ ID NO:24, or SEQ ID NO:25 and said polypeptide having monooxygenase activity has at least 70% sequence identity to an amino acid sequence set forth in SEQ ID NO: 14, SEQ ID NO: 15, SEQ ID NO: 16, SEQ ID NO:28, or SEQ ID NO:29, the recombinant host optionally further comprising an exogenous polypeptide having demethylase activity classified under EC 2.1.1.- or a polypeptide having esterase activity classified under EC 3.1.1.-, said host further producing a terminal hydroxyl C₄₋₉ hydroxyalkanoate.
 66. (canceled)
 67. A The recombinant host of claim 65, wherein said terminal hydroxyl (C₃₋₈ hydroxyalkyl)-C(═O)OCH₃ ester is 5-hydroxypentanoate methyl ester, and is enzymatically converted to 5-hydroxypentanoate using an exogenous polypeptide having demethylase activity classified under EC 2.1.1.- or a polypeptide having esterase activity classified under EC 3.1.1.-, the recombinant host optionally further comprising one or more of the following exogenous polypeptides: a polypeptide having monooxygenase activity, a polypeptide having alcohol dehydrogenase activity, a polypeptide having aldehyde dehydrogenase activity, a polypeptide having 6-hydroxyhexanoate dehydrogenase activity, a polypeptide having 5-hydroxypentanoate dehydrogenase activity, a polypeptide having 4-hydroxybutyrate dehydrogenase activity, a polypeptide having 6-oxohexanoate dehydrogenase activity, and a polypeptide having 5-oxopentanoate dehydrogenase activity, said recombinant host further producing glutarate semialdehyde or glutaric acid.
 68. (canceled)
 69. (canceled)
 70. The recombinant host of claim 67, said recombinant host further comprising an exogenous polypeptide having ω-transaminase activity, said recombinant host further producing 5-aminopentanoate, the recombinant host optionally further comprising an exogenous polypeptide having carboxylate reductase activity and an exogenous polypeptide having ω-transaminase activity and optionally one or more exogenous enzymes selected from the group consisting of a polypeptide having N-acetyl transferase activity, a polypeptide having acetylputrescine deacetylase activity, and a polypeptide having alcohol dehydrogenase activity, said host further producing cadaverine.
 71. (canceled)
 72. The recombinant host of claim 67, said recombinant host further comprising an exogenous polypeptide having carboxylate reductase activity and an exogenous polypeptide having alcohol dehydrogenase activity, said host further producing 1,5-pentanediol.
 73. The recombinant host of claim 67, said recombinant host further comprising (i) an exogenous polypeptide having β-ketothiolase activity or an exogenous polypeptide having acetyl-CoA carboxylase activity and an exogenous polypeptide having β-ketoacyl-[acp] synthase activity, (ii) an exogenous polypeptide having 3-hydroxyacyl-CoA dehydrogenase activity or an exogenous polypeptide having 3-oxoacyl-CoA reductase activity, (iii) an exogenous polypeptide having enoyl-CoA hydratase activity and (iv) an exogenous polypeptide having trans-2-enoyl-CoA reductase activity, the recombinant host optionally further comprising (v) an exogenous polypeptide having thioesterase activity or (vi) an exogenous polypeptide having butanal dehydrogenase activity and an exogenous polypeptide having aldehyde dehydrogenase activity.
 74. (canceled)
 75. A recombinant host comprising at least one exogenous nucleic acid encoding (i) a polypeptide having alcohol O-acetyltransferase activity and (ii) a polypeptide having monooxygenase activity, and producing any of a (C₄₋₉ alkyl)-OC(═O)—(C₃₋₈ hydroxyalkyl) ester, a (C₄₋₉ hydroxyalkyl)-OC(═O)—(C₃₋₈ hydroxyalkyl) ester, or a (C₄₋₉ hydroxyalkyl)-OC(═O)—(C₃₋₈ alkyl) ester, wherein said polypeptide having alcohol O-acetyltransferase activity has at least 70% sequence identity to the amino acid sequence set forth in SEQ ID NO: 26 and said monooxygenase has at least 70% sequence identity to an amino acid sequence set forth in SEQ ID NO: 14, SEQ ID NO: 15, SEQ ID NO: 16, SEQ ID NO:28, and SEQ ID NO:29, wherein said (C₄₋₉ alkyl)-OC(═O)—(C₃₋₈ hydroxyalkyl) ester is pentanoic acid 5-hydroxypentyl ester, said (C₄₋₉ hydroxyalkyl)-OC(═O)—(C₃₋₈ hydroxyalkyl) ester is 5-hydroxypentanoic acid 5-hydroxypentyl ester, and said (C₄₋₉ hydroxyalkyl)-OC(═O)—(C₃₋₈ alkyl) ester is 5-hydroxypentanoic acid pentyl ester, the recombinant host optionally further comprising an exogenous polypeptide having esterase activity and further enzymatically converting pentanoic acid 5-hydroxypentyl ester, 5-hydroxypentanoic acid 5-hydroxypentyl ester, and 5-hydroxypentanoic acid pentyl ester to 5-hydroxypentanoate and/or 1,5-pentanediol, wherein said polypeptide having esterase activity has at least 70% sequence identity to an amino acid sequence set forth in SEQ ID NO:
 27. 76. (canceled)
 77. (canceled)
 78. The recombinant host of claim 75, said recombinant host further comprising one or more exogenous polypeptides selected from the group consisting of a polypeptide having monooxygenase activity, a polypeptide having alcohol dehydrogenase activity, a polypeptide having aldehyde dehydrogenase activity, a polypeptide having 6-hydroxyhexanoate dehydrogenase activity, a polypeptide having 5-hydroxypentanoate dehydrogenase activity, a polypeptide having 4-hydroxybutyrate dehydrogenase activity, a polypeptide having 5-oxopentanoate dehydrogenase activity, a polypeptide having 6-oxohexanoate dehydrogenase activity, and a polypeptide having 7-oxoheptanoate dehydrogenase activity, said host further producing glutarate semialdehyde or glutaric acid, the recombinant host optionally further comprising an exogenous polypeptide having ω-transaminase activity, said host further producing 5-aminopentanoate.
 79. (canceled)
 80. The recombinant host of claim 78, said recombinant host further comprising an exogenous polypeptide having carboxylate reductase activity and an exogenous polypeptide having ω-transaminase activity and optionally one or more of the following exogenous polypeptides: a polypeptide having N-acetyl transferase activity, a polypeptide having deacetylase activity, and a polypeptide having alcohol dehydrogenase activity, said host further producing cadaverine.
 81. The recombinant host of claim 75, said recombinant host further comprising: one or more exogenous polypeptides selected from the group consisting of (i) a polypeptide having β-ketothiolase activity or a polypeptide having acetyl-CoA carboxylase activity and a polypeptide having β-ketoacyl-[acp] synthase activity, (ii) a polypeptide having 3-hydroxyacyl-CoA dehydrogenase activity or a polypeptide having 3-oxoacyl-CoA reductase activity, (iii) a polypeptide having enoyl-CoA hydratase activity, and (iv) a polypeptide having trans-2-enoyl-CoA reductase activity; or one or more exogenous polypeptides selected from the group consisting of a polypeptide having carboxylate reductase activity, a polypeptide having aldehyde dehydrogenase activity, a polypeptide having butanal dehydrogenase activity, and a polypeptide having alcohol dehydrogenase activity.
 82. (canceled)
 83. A bio-derived product, bio-based product or fermentation-derived product, wherein said product comprises: (i) a composition comprising at least one bio-derived, bio-based or fermentation-derived compound according to claim 1; (ii) a bio-derived, bio-based or fermentation-derived polymer comprising the bio-derived, bio-based or fermentation-derived composition or compound of (i), or any a combination thereof; (iii) a bio-derived, bio-based or fermentation-derived resin comprising the bio-derived, bio-based or fermentation-derived compound or bio-derived, bio-based or fermentation-derived composition of (i) or any combination thereof or the bio-derived, bio-based or fermentation-derived polymer of (ii) or a combination thereof; (iv) a molded substance obtained by molding the bio-derived, bio-based or fermentation-derived polymer of (ii) or the bio-derived, bio-based or fermentation-derived resin of (iii), or a combination thereof; (v) a bio-derived, bio-based or fermentation-derived formulation comprising the bio-derived, bio-based or fermentation-derived composition of (i), bio-derived, bio-based or fermentation-derived compound of (i), bio-derived, bio-based or fermentation-derived polymer of (ii), bio-derived, bio-based or fermentation-derived resin of (iii), or bio-derived, bio-based or fermentation-derived molded substance of (iv), or a combination thereof; or (vi) a bio-derived, bio-based or fermentation-derived semi-solid or a non-semi-solid stream, comprising the bio-derived, bio-based or fermentation-derived composition of (i), bio-derived, bio-based or fermentation-derived compound of (i), bio-derived, bio-based or fermentation-derived polymer of (ii), bio-derived, bio-based or fermentation-derived resin of (iii), bio-derived, bio-based or fermentation-derived formulation of (v), or bio-derived, bio-based or fermentation-derived molded substance of (iv), or a combination thereof. 